Publications

Publications in the field of Molecular Dynamics and Biomolecular Theory by W.F. van Gunsteren/P.H. Hünenberger (ETH Zürich), A.E. Mark (University of Queensland, AUS), S.J. Marrink/A.H. de Vries (University of Groningen, NL) and co-workers

in press
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1977-1981

77.1
W.F. van Gunsteren and H.J.C. Berendsen
Algorithms for macromolecular dynamics and constraint dynamics
Mol. Phys. 34 (1977) 1311-1327

77.2
J.-P. Ryckaert, G. Ciccotti, H.J.C. Berendsen
Numerical Integration of the Cartesian Equations of Motion of a
System with Constraints: Molecular Dynamics of n-Alkanes
J. Comput. Phys. 23 (1977) 327-341

78.1
W.G.J. Hol, P.T. van Duijnen and H.J.C. Berendsen
The alpha-helix dipole and the properties of proteins
Nature 273 (1978) 443-446

78.2
W.F. van Gunsteren, H.J.C. Berendsen and J.A.C. Rullmann
Inclusion of Reaction Fields in Molecular Dynamics: Application to Liquid Water
Faraday Disc. Chem. Soc. 66 (1978) 58-70

78.3
T. Lee, J. Bisschop, W. van der Lugt and W.F. van Gunsteren
Radial distribution functions of liquid Na and Cs
Physica 93B (1978) 59-62

80.1
P. van der Ploeg and H.J.C. Berendsen
Molecular dynamics of model membranes
Biophys. Struct. Mechanisms 6 Suppl. (1980) 106 (abstract)

80.2
W.F. van Gunsteren
Constrained dynamics of flexible molecules
Mol. Phys. 40 (1980) 1015-1019

80.3
W.F. van Gunsteren and M. Karplus
A Method for Constrained Energy Minimization of Macromolecules
J. Comput. Chem. 1 (1980) 266-274

81.1
H.J.C. Berendsen
Moleculaire dynamica, Perspectief voor complexe systemen (in Dutch)
Chemisch Magazine, juli/aug. 1981, 403 and sept. 1981, 461-464

81.2
W.F. van Gunsteren, H.J.C. Berendsen and J.A.C. Rullmann
Stochastic dynamics for molecules with constraints Brownian dynamics of n-alkanes
Mol. Phys. 44 (1981) 69-95

81.3
W.F. van Gunsteren and M. Karplus
Effect of constraints, solvent and crystal environment on protein dynamics
Nature 293 (1981) 677-678

81.4
H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren and J. Hermans
Interaction models for water in relation to protein hydration
In: "Intermolecular Forces", B. Pullman ed., Reidel, Dordrecht, 1981, p. 331-342

1982

82.1
P. van der Ploeg and H.J.C. Berendsen
Molecular dynamics simulation of a bilayer membrane
J. Chem. Phys. 76 (1982) 3271-3276

82.2
P. van der Ploeg
Molecular Dynamics of Membranes
Thesis, University of Groningen, July 1982

82.3
W.F. van Gunsteren and H.J.C. Berendsen
Algorithms for brownian dynamics
Mol. Phys. 45 (1982) 637-647

82.4
W.F. van Gunsteren and H.J.C. Berendsen
Molecular dynamics: perspective for complex systems
Biochem. Soc. Trans. 10 (1982) 301-305

82.5
W.F. van Gunsteren and H.J.C. Berendsen
On the fluctuation-dissipation theorem for interacting brownian particles
Mol. Phys. 47 (1982) 721-723

82.6
J.P.M. Postma, H.J.C. Berendsen and J.R. Haak
Thermodynamics of Cavity Formation in Water: A Molecular Dynamics Study
Faraday Symp. Chem. Soc. 17 (1982) 55-67

82.7
S. Swaminathan, T. Ichiye, W.F. van Gunsteren and M. Karplus
Time Dependence of Atomic Fluctuations in Proteins: Analysis of Local and Collective Motions in Bovine Pancreatic Trypsin Inhibitor
Biochemistry 21 (1982) 5230-5241

82.8
W.F. van Gunsteren and M. Karplus
Effect of Constraints on the Dynamics of Macromolecules
Macromolecules 15 (1982) 1528-1544

82.9
W.F. van Gunsteren and M. Karplus
Protein Dynamics in Solution and in a Crystalline Environment: A Molecular Dynamics Study
Biochemistry 21 (1982) 2259-2274

1983

83.2
P. van der Ploeg and H.J.C. Berendsen
Molecular dynamics of a bilayer membrane
Mol. Phys. 49 (1983) 233-248

83.2
W.F. van Gunsteren, H.J.C. Berendsen, J. Hermans, W.G.J. Hol and J.P.M. Postma
Computer simulation of the dynamics of hydrated protein crystals and its comparison with X-ray data
Proc. Natl. Acad. Sci USA 80 (1983) 4315-4319

83.3
O. Edholm, H.J.C. Berendsen and P. van der Ploeg
Conformational entropy of a bilayer membrane derived from a molecular dynamics simulation
Mol. Phys. 48 (1983) 379-388

83.4
H.J.C. Berendsen and W.F. van Gunsteren
Molecular dynamics with constraints
In: "The Physics of Superionic Conductors and Electrode Materials", J.W. Perram, ed., NATO ASI Series B92 (1983) 221-240 (Plenum Press)

83.5
W.F. van Gunsteren and H.J.C. Berendsen
Stochastic dynamics of polymers
In: "The Physics of Superionic Conductors and Electrode Materials", J.W. Perram, ed., NATO ASI Series B92 (1983) 241-256 (Plenum Press)

83.6
M. Karplus, S. Swaminathan, T. Ichiye and W.F. van Gunsteren
Local and collective motions in protein dynamics
In: "Mobility and function in proteins and nucleic acids", Ciba Symp. 93 , Pitman, London, (1983), pp. 271-290

83.7
H.J.C. Berendsen
Discussion note in "Mobility and function in proteins and nucleic acids", Ciba Symp. 93, Pitman, London, (1983), pp. 283-284

1984

84.1
J. Hermans, H.J.C. Berendsen, W.F. van Gunsteren and J.P.M. Postma
A Consistent Empirical Potential for Water-Protein Interactions
Biopolymers 23 (1984) 1513-1518

84.2
H.J.C. Berendsen, W.F. van Gunsteren and J.P.M. Postma
Molecular Dynamics on CRAY, CYBER and DAP
In: "High-Speed Computation", J.S. Kowalik, ed., NATO ASI Series F7 (1984) 425-438 (Springer, Berlin)

84.3
W.F. van Gunsteren, H.J.C. Berendsen, F. Colonna, D. Perahia, J.P. Hollenberg and D. Lellouch
On Searching Neighbours in Computer Simulations of Macromolecular Systems
J. Comput. Chem. 5 (1984) 272-279

84.4
W.F. van Gunsteren and H.J.C. Berendsen
Computer Simulation as a Tool for Tracing the Conformational Differences between Proteins in Solution and in the Crystalline State
J. Mol. Biol. 176 (1984) 559-564

84.5
O. Edholm and H.J.C. Berendsen
Entropy estimation from simulations of non-diffusive systems
Mol. Phys. 51 (1984) 1011-1028

84.6
H.J.C. Berendsen and W.F. van Gunsteren
Molecular Dynamics Simulations: Techniques and Approaches
In: "Molecular Liquids - Dynamics and Interactions", A.J. Barnes et al. eds., NATO ASI Series C135 (1984) 475-500 (Reidel, Dordrecht)

84.7
H.J.C. Berendsen
Survey of Future Developments in Molecular Dynamics
In: "Molecular Liquids - Dynamics and Interactions", A.J. Barnes et al. eds., NATO ASI Series C135 (1984) 561-564 (Reidel, Dordrecht)

84.8
A. DiNola, H.J.C. Berendsen and O. Edholm
Free Energy Determination of Polypeptide Conformations Generated by Molecular Dynamics
Macromolecules 17 (1984) 2044-2050

84.9
H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola and J.R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) 3684-3690

84.10
K. Remerie, W.F. van Gunsteren, J.P.M. Postma, H.J.C. Berendsen and J.B.F.N. Engberts
Molecular dynamics computer simulation of the hydation of two simple organic solutes. Comparison with the simulation of an empty cavity
Mol. Phys. 53 (1984) 1517-1526

84.11
J.P.M. Postma, H.J.C. Berendsen and T.P. Straatsma
Intramolecular vibrations from molecular dynamics simulations of liquid water
Journal de Physique C7 (1984) 31-40

84.12
W.F. van Gunsteren, R. Kaptein and E.R.P. Zuiderweg
Use of Molecular Dynamics Computer Simulations When Determining Protein Structure by 2D NMR
In: "Proceedings NATO/CECAM workshop on nucleic acid conformation and dynamics", W.K. Olson ed., 1984, Orsay, 79-92 (CECAM, France)

1985

85.1
R. Kaptein, E.R.P. Zuiderweg, R.M. Scheek, R. Boelens and W.F. van Gunsteren
A Protein Structure from Nuclear Magnetic Resonance Data lac Repressor Headpiece
J. Mol. Biol. 182 (1985) 179-182

85.2
J. Åqvist, W.F. van Gunsteren, M. Leijonmarck and O. Tapia
A Molecular Dynamics Study of the C-terminal Fragment of the L7/12 Ribosomal Protein Secondary Structure Motion in a 150 Picosecond Trajectory
J. Mol. Biol. 183 (1985) 461-477

85.3
E.R.P. Zuiderweg, R.M. Scheek, R. Boelens, W.F. van Gunsteren and R. Kaptein
Determination of protein structures from nuclear magnetic resonance data using a restrained molecular dynamics approach: The lac repressor DNA binding domain
Biochimie 67 (1985) 707-715

85.4
B. Witholt, W.F. van Gunsteren and W.G.J. Hol
Protein Engineering
In: "Proceedings of the Third European Congress on Biotechnology" Vol. IV, Verlag Chemie, Weinheim, FRG, 1985, pp. 497-517

85.5
W.F. van Gunsteren and H.J.C. Berendsen
Molecular Dynamics Simulations: Techniques and Applications to Proteins,
In: "Molecular Dynamics and Protein Structure", J. Hermans ed., Polycrystal Book Service, P.O. Box 27, Western Springs, Ill. 60558, USA, (1985), pp. 5-14

85.6
W.F. van Gunsteren, R. Boelens, R. Kaptein, R.M. Scheek and E.R.P. Zuiderweg
An Improved Restrained Molecular Dynamics Technique to Obtain Protein Tertiary Structure from Nuclear Magnetic Resonance Data
In: "Molecular Dynamics and Protein Structure", J. Hermans ed., Polycrystal Book Service, P.O. Box 27, Western Springs, Ill. 60558, USA, (1985), pp. 92-99

85.7
I. Haneef, I.D. Glover, I.J. Tickle, D.S. Moss, S.P. Wood, T.L. Blundell and W.F. van Gunsteren
The Dynamics of Pancreatic Polypeptide: A Comparison of X-ray Anisotropic Refinement at 0.98 K Resolution, Molecular Dynamics and Normal Mode Analysis
In: "Molecular Dynamics and Protein Structure", J. Hermans ed., Polycrystal Book Service, P.O. Box 27, Western Springs, Ill. 60558, USA, (1985), pp. 85-91

85.8
J. Åqvist, W.F. van Gunsteren, M. Leijonmarck and O. Tapia
A Molecular Dynamics Study of the C-terminal Fragment of the L7/L12 Ribosomal Protein
In: "Molecular Dynamics and Protein Structure", J. Hermans ed., Polycrystal Book Service, P.O. Box 27, Western Springs, Ill. 60558, USA, (1985), pp. 145-147

85.9
W.F. van Gunsteren, H.J.C. Berendsen and J.P. Hollenberg
Prospects for complex molecular systems
Supercomputer 7 (1985) 26-36

85.10
R.M. Scheek, E.R.P. Zuiderweg, R. Boelens, W.F. van Gunsteren and R. Kaptein
The Tertiary Structure of the Lac Repressor Headpiece Derived from Nuclear Magnetic Resonance Spectroscopy
In: "Magnetic resonance in Biology and Medicine", G. Govil, C.L. Khetrapal, A. Saran eds., McGraw-Hill Publ. Comp., New Delhi, India, (1985), pp. 293-303

85.11
P. Kruger, W. Strassburger, A. Wollmer and W.F. van Gunsteren
A comparison of the structure and dynamics of avian pancreatic polypeptide hormone in solution and in the crystal
Eur. Biophys. J. 13 (1985) 77-88

85.12
J.P.M. Postma
MD of H2O, a molecular dynamics study of water
Thesis, University of Groningen, 1985

85.13
H.J.C. Berendsen
Treatment of Long-Range Forces in Molecular Dynamics
In: "Molecular Dynamics and Protein Structure", J. Hermans ed., Polycrystal Book Service, P.O. Box 27, Western Springs, Ill. 60558, USA, (1985), pp. 18-22

85.14
H.J.C. Berendsen
Molecular Dynamics on Vector Processors and Special-Purpose Computers
In: "Molecular Dynamics and Protein Structure", J. Hermans ed., Polycrystal Book Service, P.O. Box 27, Western Springs, Ill. 60558, USA, (1985), pp. 123-125

85.15
H.J.C. Berendsen
Simuleren: een gebied met toekomst (in Dutch)
Chemisch Magazine, oktober 1985, 688-690

85.16
K. Remerie, W.F. van Gunsteren and J.B.F.N. Engberts
A molecular dynamics computer simulation study of the hydration of bis(methylsulfonyl)methane in water
Mol. Phys. 56 (1985) 1393-1409

85.17
K. Remerie, W.F. van Gunsteren and J.B.F.N. Engberts
Molecular dynamics computer simulation as a tool for the analysis of solvation. A study of dilute aqueous solutions of 1,4-dioxane and 1,3-dioxane
Recl. Trav. Chim. Pays-Bas 104 (1985) 79-89

85.18
H.J.C. Berendsen, J.P.M. Postma and W.F. van Gunsteren
Statistical Mechanics and Molecular Dynamics: The Calculation of Free Energy
In: "Molecular Dynamics and Protein Structure", J. Hermans ed., Polycrystal Book Service, P.O. Box 27, Western Springs, Ill. 60558, USA, (1985), pp. 43-46

85.19
H. Kessler, B. Kutscher, R. Kerssebaum, A. Klein, J. Lautz, R. Obermeier, H. Muellner, W.F. van
Design, synthesis and conformation of superactive thymopoietin-analogues
In: "Peptides, Structure and Function, Proceedings of the Ninth American Peptide Symposium", C.M. Deber, V.J. Hruby and K.D. Kopple eds., Pierce Chemical, (1985) pp. 83-92

1986

86.1
W.F. van Gunsteren
Ontwerpen van medicijnen en gemodificeerde enzymen met behulp van computersimulatie (in Dutch)
Biotechnologie in Nederland 1 (1986) 13-15

86.2
R.G. Geurtsen and J.P. Hollenberg
Vectorization of the calculation of nonbonded interactions
Supercomputer 11 (1986) 15-25

86.3
H.J.C. Berendsen and W.G.J. Hol
Long-Range Electrostatic Forces
Europhysics News 17 (1986) 8-10

86.4
K. Remerie, J.B.F.N. Engberts and W.F. van Gunsteren
A molecular dynamics computer simulation study of the temperature dependence of hydration of 1,4-dioxane and 1,3-dioxane
Chemical Physics 101 (1986) 27-44

86.5
T.P. Straatsma, H.J.C. Berendsen and A.J. Stam
Estimation of statistical errors in molecular simulation calculations
Mol. Phys. 57 (1986) 89-95

86.6
P. Sandblom, J. Åqvist, T.A. Jones, M.E. Newcomer, W.F. van Gunsteren and O. Tapia
Structural Changes in Retinol Binding Protein Induced by Retinol Removal. A Molecular Dynamics Study
Biochem. and Biophys. Research Comm. 139 (1986) 564-570

86.7
H.J.C. Berendsen and W.F. van Gunsteren
Practical Algorithms for Dynamic Simulations
In: "Molecular-Dynamics Simulation of Statistical-Mechanical Systems", Proceedings of the International School of Physics "Enrico Fermi", course 97, G. Ciccotti and W.G. Hoover eds., (1986), North-Holland, Amsterdam, pp. 43-65

86.8
H.J.C. Berendsen
Biological Molecules and Membranes
In: "Molecular-Dynamics Simulation of Statistical-Mechanical Systems", Proceedings of the International School of Physics "Enrico Fermi", course 97, G. Ciccotti and W.G. Hoover eds., (1986), North-Holland, Amsterdam, pp. 496-519

86.9
T.P. Straatsma, H.J.C. Berendsen and J.P.M. Postma
Free energy of hydrophobic hydration: A molecular dynamics study of noble gases in water
J. Chem. Phys. 85 (1986) 6720-6727

86.10
J. Åqvist, P. Sandblom, T.A. Jones, M.E. Newcomer, W.F. van Gunsteren and O. Tapia
Molecular Dynamics Simulations of the Holo and Apo Forms of Retinol Binding Protein Structural and Dynamical Changes Induced by Retinol Removal
J. Mol. Biol. 192 (1986) 593-604

86.11
H.J.C. Berendsen, W.F. van Gunsteren, H.R.J. Zwinderman and R.G. Geurtsen
Simulations of Proteins in Water
Ann. New York Acad. Sci. 482 (1986) 269-285

86.12
W.F. van Gunsteren, H.J.C. Berendsen, R.G. Geurtsen and H.R.J. Zwinderman
A Molecular Dynamics Computer Simulation of an Eight-Base-Pair DNA Fragment in Aqueous Solution: Comparison with Experimental Two-Dimensional NMR Data
Ann. New York Acad. Sci. 482 (1986) 287-303

86.13
H.J.C. Berendsen and B. Egberts
Molecular Dynamics of a Bilayer Membrane with Atomic Detail
In: Springer Series in Biophysics, Vol. 1, "Structure, Dynamics and Function of Biomolecules", A. Ehrenberg, R. Rigler, A. Graslund, L. Nilsson eds., (1986), Springer, pp. 275-280

86.14
J. de Vlieg, R. Boelens, R.M. Scheek, R. Kaptein and W.F. van Gunsteren
Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data: A Lac Repressor Headpiece Structure Based on Information on J-coupling and from Presence and Absence of NOE's
Isr. Journal of Chemistry 27 (1986) 181-188

1987

87.1
W.F. van Gunsteren
Molecular dynamics of proteins and nucleic acids
Fres. Z. Anal. Chem. 327 (1987) 69-70

87.2
W.F. van Gunsteren and H.J.C. Berendsen
Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry
J. Computer-Aided Mol. Design 1 (1987) 171-176

87.3
P. Kruger, W. Strassburger, A. Wollmer, W.F. van Gunsteren and G.G. Dodson
The simulated dynamics of the insulin monomer and their relationship to the molecule's structure
Eur. Biophys. J. 14 (1987) 449-459

87.4
H.J.C. Berendsen
Biophysical applications of molecular dynamics
Comput Phys. Comm. 44 (1987) 233-242

87.5
H.J.C. Berendsen, J.R. Grigera and T.P. Straatsma
The Missing Term in Effective Pair Potentials
J. Phys. Chem. 91 (1987) 6269-6271

87.6
J. Koehler, W. Saenger and W.F. van Gunsteren
A molecular dynamics simulation of crystalline alpha-cyclodextrin hexahydrate
Eur. Biophys. J. 15 (1987) 197-210

87.7
J. Koehler, W. Saenger and W.F. van Gunsteren
Molecular dynamics simulation of crystalline ß-cyclodextrin dodecahydrate at 293 K and 120 K
Eur. Biophys. J. 15 (1987) 211-224

87.8
J. Lautz, H. Kessler, R. Boelens, R. Kaptein and W.F. van Gunsteren
Conformational analysis of a cyclic thymopoietin-analogue by 1H n.m.r. spectroscopy and restrained molecular dynamics simulations
Int. J. Peptide Protein Res. 30 (1987) 404-414

87.9
H.J.C. Berendsen, W.F. van Gunsteren, E. Egberts and J. de Vlieg
Dynamic Simulation of Complex Molecular Systems
ACS Symposium Series 353, "Supercomputer Research in Chemistry and Chemical Engineering", K.F. Jensen and D.G. Truhlar eds., Am. Chem. Soc., Washington D.C., 1987, pp. 106-122

87.10
T.P. Straatsma
Free energy evaluation by molecular dynamics simulations
Thesis, University of Groningen, December 1987

87.11
P. Kollman and W.F. van Gunsteren
Molecular Mechanics and Dynamics in Protein Design
Methods in Enzymology Vol 154, Recombinant DNA, Part E, R. Wu and L. Grossman eds.,(1987), pp. 430-449 (Academic Press)

87.12
J. Lautz, H. Kessler, R. Kaptein and W.F. van Gunsteren
Molecular dynamics simulations of cyclosporin A: The crystal structure and dynamic modelling of a structure in apolar solution based on NMR data
J. Computer-Aided Mol. Design 1 (1987) 219-241

87.13
W.F. van Gunsteren, J.E.H. Koehler and W. Saenger
On the Difference between Molecular Conformation and Hydrogen Bonding in Solution and in Crystalline State
Proceedings of the XXXV-th Colloquium Protides of the Biological Fluids, Brussels, April 1987, Pergamon, Oxford, 35 (1987) 489-492

1988

88.1
H. Pepermans, D. Tourwe, G. van Binst, R. Boelens, R.M. Scheek, W.F. van Gunsteren and R.
The Combined Use of NMR, Distance Geometry, and Restrained Molecular Dynamics for the Conformational Study of a Cyclic Somatostatin Analogue
Biopolymers 27 (1988) 323-338

88.2
W.F. van Gunsteren and H.J.C. Berendsen
A leap-frog algorithm for stochastic dynamics
Molecular Simulation 1 (1988) 173-185

88.3
W.F. van Gunsteren
The role of computer simulation techniques in protein engineering
Protein Engineering 2 (1988) 5-13

88.4
Shi Yun-yu, Yun Ru-huai and W.F. van Gunsteren
Molecular Dynamics Simulation of Despentapeptide Insulin in a Crystalline Environment
J. Mol. Biol. 200 (1988) 571-577

88.5
H. Kessler, C. Griesinger, J. Lautz, A. Mueller, W.F. van Gunsteren and H.J.C. Berendsen
Conformational Dynamics Detected by Nuclear Magnetic Resonance NOE Values and J-Coupling Constants
J.Am.Chem.Soc. 110 (1988) 3393-3396

88.6
J. de Vlieg, R.M. Scheek, W.F. van Gunsteren, H.J.C. Berendsen, R. Kaptein and J. Thomason
Combined Procedure of Distance Geometry and Restrained Molecular Dynamics Techniques for Protein Structure Determination From Nuclear Magnetic Resonance Data: Application to the DNA Binding Domain of Lac Repressor From Escherichia Coli
Proteins 3 (1988) 209-218

88.7
J.E.H. Koehler, W. Saenger and W.F. van Gunsteren
On the Occurrence of Three-Center Hydrogen Bonds in Cyclodextrins in Crystalline Form and in Aqueous Solution: Comparison of Neutron Diffraction and Molecular Dynamics Results
J. Biomol. Struct. Dyn. 6 (1988) 181-198

88.8
W. Soppe, C. van der Marel, W.F. van Gunsteren and H.W. den Hartog
New insights into the structure of B2O3 glass
J. of Non-Crystalline Solids 103 (1988) 201-209

88.9
R. Kaptein, R. Boelens, R.M. Scheek and W.F. van Gunsteren
Protein Structures from NMR
Biochemistry 27 (1988) 5389-5395

88.10
J.E.H. Koehler, W. Saenger and W.F. van Gunsteren
The flip-flop hydrogen bonding phenomenon Molecular dynamics simulation of crystalline ß-cyclodextrin
Eur. Biophys. J. 16 (1988) 153-168

88.11
J.E.H. Koehler, W. Saenger and W.F. van Gunsteren
Conformational Differences Between Alpha-Cyclodextrin in Aqueous Solution and in Crystalline Form: A Molecular Dynamics Study
J. Mol. Biol. 203 (1988) 241-250

88.12
E. Egberts and H.J.C. Berendsen
Molecular dynamics simulation of a smectic liquid crystal with atomic detail
J. Chem. Phys. 89 (1988) 3718-3732

88.13
H.J.C. Berendsen
Dynamic simulation as an essential tool in molecular modeling
J. Computer-Aided Mol. Design 2 (1988) 217-221

88.14
Shi Yun-yu, Wang Lu and W.F. van Gunsteren
On the approximation of solvent effects on the conformation and dynamics of cyclosporin A by stochastic dynamics simulation techniques
Molecular Simulation 1 (1988) 369-383

88.15
W.F. van Gunsteren
Classical molecular dynamics simulations: algorithms and applications, stochastic dynamics, and free energies
In: "Mathematical Frontiers in Computational Chemical Physics", D.G. Truhlar ed., The IMA Volumes in Mathematics and its Applications, Vol. 15 (1988) Springer, New York, pp. 136-156

88.16
T.P. Straatsma and H.J.C. Berendsen
Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations
J. Chem. Phys. 89 (1988) 5876-5886

88.17
A.E. Torda, B.C. Mabbutt, W.F. van Gunsteren and R.S. Norton
Backbone folding of the polypeptide cardiac stimulant anthopleurin-A determined by nuclear magnetic resonance, distance geometry and molecular dynamics
FEBS Letters 239 (1988) 266-270

88.18
E. Egberts
Molecular Dynamics Simulation of Multibilayer Membranes
Thesis, University of Groningen, November 1988

1989

89.1
W.F. van Gunsteren
Methods for calculation of free energies and binding constants: Successes and problems
In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", W.F. van Gunsteren and P.K. Weiner eds., Escom Science Publishers, Leiden, The Netherlands, (1989), pp. 27-59

89.2
M. Fujinaga, P. Gros and W.F. van Gunsteren
Testing the Method of Crystallographic Refinement Using Molecular Dynamics
J. Appl. Cryst. 22 (1989) 1-8

89.3
P. Gros, M. Fujinaga, B.W. Dijkstra, K.H. Kalk and W.G.J. Hol
Molecular dynamics refinement of the X-ray structure of thermitase complexed with eglin-c
In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", W.F. van Gunsteren and P.K. Weiner eds., Escom Science Publishers, Leiden, The Netherlands, (1989), pp. 190-193

89.4
A.E. Torda, R.M. Scheek and W.F. van Gunsteren
Time-dependent distance restraints in molecular dynamics simulations
Chem. Phys. Letters 157 (1989) 289-294

89.5
J. Lautz, H. Kessler, J.M. Blaney, R.M. Scheek and W.F. van Gunsteren
On calculating three-dimensional molecular structure from atom-atom distance information: cyclosporin A
Int. J. Peptide Protein Res. 33 (1989) 281-288

89.6
J. de Vlieg
Molecular Dynamics Computer Simulations based on NMR Data: Application to the DNA binding domain of lac repressor and its operator
Thesis, University of Groningen, May 1989

89.7
W.F. van Gunsteren
Computer simulation by molecular dynamics as a tool for modelling of molecular systems
Molecular Simulation 3 (1989) 187-200

89.8
M.W. Makinen, J.M. Troyer, H. van der Werff, H.J.C. Berendsen and W.F. van Gunsteren
Dynamical Structure of Carboxypeptidase A
J. Mol. Biol. 207 (1989) 201-216

89.9
P. Gros, M. Fujinaga, A. Mattevi, F.M.D. Vellieux, W.F. van Gunsteren and W.G.J. Hol
Protein Structure Refinement by Molecular Dynamics Techniques
In: "Molecular Simulation and Protein Crystallography, Proceedings of the Joint CCP4/CCP5 Study Weekend 27-28 January", 1989, J. Goodfellow, K. Henrick and R.
Hubbard eds., SERC, Daresbury, 1989

89.10
S.J. Picken, W.F. van Gunsteren, P.Th. van Duijnen and W.H. de Jeu
A molecular dynamics study of the nematic phase of 4-n-pentyl-4'-cyanobiphenyl
Liquid Crystals 6 (1989) 357-371

89.11
J. de Vlieg, H.J.C. Berendsen and W.F. van Gunsteren
An NMR Based Molecular Dynamics Simulation of the Interaction of the lac Repressor Headpiece and Its Operator in Aqueous Solution
Proteins 6 (1989) 104-127

89.12
P. Gros, M. Fujinaga, B.W. Dijkstra, K.H. Kalk and W.G.J. Hol
Crystallographic Refinement by Incorporation of Molecular Dynamics: Thermostable Serine Protease Thermitase Complexed with Eglin c
Acta Cryst. B45 (1989) 488-499

89.13
R.M. Scheek, W.F. van Gunsteren and R. Kaptein
Molecular Dynamics Simulation Techniques for Determination of Molecular Structures from Nuclear Magnetic Resonance Data
In: Methods in Enzymology, Vol. 177, "Nuclear Magnetic Resonance, Part B: Structure and Mechanism", N.J. Oppenheimer and T.L. James eds., (1989) 204-218 (Academic Press)

89.14
J. Lautz, H. Kessler, W.F. van Gunsteren, H.J.C. Berendsen, R.M. Scheek, R. Kaptein and J.M. Blaney
Restrained Molecular Dynamics Simulations of Cyclic Peptides
In: "Proceedings of the 20-th European Peptide Symposium (1988)", G. Jung and E. Bayer eds., (1989), pp. 438-440

1990

90.1
W.F. van Gunsteren
On testing theoretical models by comparison of calculated with experimental data
In: Studies in Physical and Theoretical Chemistry, Vol 71, Modelling of Molecular Structures and Properties, J.-L. Rivail ed., Elsevier, Amsterdam, 1990, pp. 463-478

90.2
A.E. Torda, R.M. Scheek and W.F. van Gunsteren
Time-averaged Nuclear Overhauser Effect Distance Restraints Applied to Tendamistat
J. Mol. Biol. 214 (1990) 223-235

90.3
J. Lautz, H. Kessler, W.F. van Gunsteren, H.-P. Weber and R.M. Wenger
On the Dependence of Molecular Conformation on the Type of Solvent Environment: A Molecular Dynamics Study of Cyclosporin A
Biopolymers 29 (1990) 1669-1687

90.4
P. Gros
Studies in Protein Crystallography & Dynamics: On Membrane Protein Crystallization, the Structure of Thermitase - Eglin and the Application of Molecular Dynamics
Thesis, University of Groningen, August 1990

90.5
P. Gros, W.F. van Gunsteren and W.G.J. Hol
Inclusion of Thermal Motion in Crystallographic Structures by Restrained Molecular Dynamics
Science 249 (1990) 1149-1152

90.6
W.F. van Gunsteren and H.J.C. Berendsen
Computer Simulation of Molecular Dynamics: Methodology, Applications and Perspectives in Chemistry
Angew. Chem. Int. Ed. Engl. 29 (1990) 992-1023

90.7
J. de Vlieg, H.J.C. Berendsen and W.F. van Gunsteren
Structure of lac Repressor Headpiece-Operator Complex in Aqueous Solution
In: "Frontiers in Drug Research", Alfred Benzon Symposium 28, B. Jensen, F.S. Jorgensen, H. Kofod eds., Munksgaard, Copenhagen, (1990), pp. 362-368

90.8
O. Nilsson, O. Tapia and W.F. van Gunsteren
Structure and Fluctuations of Bacteriophage T4 Glutaredoxin Modelled by Molecular Dynamics
Biochem. and Biophys. Research Comm. 171 (1990) 581-588

90.9
C.P.M. van Mierlo, P. Lijnzaad, J. Vervoort, F. Mueller, H.J.C. Berendsen and J. de Vlieg
Tertiary structure of two-electron reduced Megasphaera elsdenii flavodoxin and some implications, as determined by two-dimensional 1H NMR and restrained molecular dynamics
Eur. J. Biochem. 194 (1991) 185-198

1991

91.1
A.E. Torda and W.F. van Gunsteren
The Refinement of NMR structures by Molecular Dynamics Simulation
Computer Phys. Comm. 62 (1991) 289-296

91.2
A.E. Mark, W.F. van Gunsteren and H.J.C. Berendsen
Calculation of Relative Free Energy via Indirect Pathways
J. Chem. Phys. 94 (1991) 3808-3816

91.3
A.E. Mark, H.J.C. Berendsen, A.P. Heiner and W.F. van Gunsteren
Calculation of Relative Free Energy by Molecular Dynamics
Proc. 7th Intl. Symp. on "Methabolism and Enzymology of Nucleic Acids Including Gene and Protein Engineering"
J.Balan, ed., Inst. of Mol. Biol. Slovak Academy of Sciences, Bratislava (1991) pp. 25-38

91.4
H.J.C. Berensen
Incomplete equilibration: A source of error in free energy calculations in:
"Proteins: Structure, Dynamics and Design"
V. Renugopalakrishnan, P.R. Carey, I.C.P. Smith, S.G. Huang and A.C. Storer eds., ESCOM, Leiden (1991) pp. 384-392

91.5
H.J.C. Berensen
Molecular Dynamics studies of proteins and nucleic acids
Current Opinion in Struct. Biol. 1 (1991) 191-195

91.6
H.J.C. Berensen
Transport Properties computed by Linear Response through weak coupling to a bath in:
"Computer Simulation in Materials Science", M. Meyer and V. Pontikis, eds., Kluwer Academic Publishers (1991) pp. 139-155

91.7
A.H. Juffer, E.F.F. Botta, B.A.M. van Keulen, A. van der Ploeg and H.J.C. Berendsen
The Electric Potential of a Macromolecule in a Solvent: A Fundamental Approach
J. Comput. Phys. 97 (1991) 144-171

91.8
W.F. van Gunsteren
Computer Simulation of Biomolecular Systems: Overview of time-saving techniques
in: "Advances in Biomolecular Simulations", R. Lavery, J.-L. Rivail and J. Smith, eds., 1991, American Inst. of Physics (A.I.P.) Conference Proceedings, Vol. 239, New York, pp. 131-146

91.9
W.F. van Gunsteren, P. Gros, A.E. Torda, H.J.C. Berendsen and R.C. van Schaik
On deriving spatial structure from NMR or X-ray diffraction data
in: "Protein Conformation", 1991, Wiley-Interscience, Ciba Foundation Symposium 161, pp. 150-166

91.10
A.E. Mark, H.J.C. Berendsen and W.F. van Gunsteren
Conformational flexibility of aqueous monomeric and dimeric insulin: A molecular dynamics study
Biochemistry 30 (1991) 10866-10872

91.11
J. de Vlieg and W.F. van Gunsteren
Combined Procedures of Distance Geometry and Molecular Dynamics for Determining Protein Structure from Nuclear Magnetic Resonance Data
in: "Molecular Design and Modeling: Concepts and Applications, Part A: Proteins, Peptides and Enzymes", J.J. Langone ed., 1991, Academic Press Inc., Methods in Enzymology, Vol. 202, pp. 268-285

91.12
R.M. Scheek, A.E. Torda, J. Kemmink and W.F. van Gunsteren
Structure Determination by NMR: The Modelling of NMR Parameters as Ensemble Averages
in: Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, J.C. Hoch, F.M. Poulsen and C. Redfield, eds., NATO ASI Series A225, Plenum Press, New York, 1991, pp. 209-217

91.13
A.E. Torda, R.M. Scheek and W.F. van Gunsteren
Time Averaged Distance Restraints in NMR based Structural Refinement
in: Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, J.C. Hoch, F.M. Poulsen and C. Redfield, eds., NATO ASI Series A225, Plenum Press, New York, 1991, pp. 219-225

1992

92.1
W.F. van Gunsteren and A.E. Mark
On the interpretation of biochemical data by molecular dynamics computer simulation
Eur. J. Biochem. 204 (1992) 947-961

92.2
S.P. van Helden
Structure and Stability of Cyclodextrin Complexes
Thesis, University of Utrecht, April 1992

92.3
T. Vorherr, O. Kessler, A. Mark and E. Carafoli
Construction and molecular dynamics simulation of calmodulin in the extended and in a bent conformation
Eur. J. Biochem. 204 (1992) 931-937

92.4
R.C. van Schaik, W.F. van Gunsteren and H.J.C. Berendsen
Conformational Search by Potential Energy Annealing: Algorithm and Application to Cyclosporin A
J. of Computer-Aided Mol. Design 6 (1992) 97-112

92.5
W.F. van Gunsteren
Molecular Dynamics Simulation in Practice
in: Les Cahiers IMABIO, no. 4, CNRS, April 1992, pp. 27-29

92.6
R.M. Spycher, P.M. King and A. Bauder
Rotational spectrum and structure of a furan-(argon)2 van der Waals complex
Chem. Phys. Lett. 191 (1992) 102-106

92.7
F. Müller-Plathe and W.F. van Gunsteren
Molecular Simulation of Polymer-Penetrant Systems
Polymer Preprints, ACS, 1992, 633-634

92.8
W.F. van Gunsteren, R.M. Brunne, A.E. Mark and S.P. van Helden
Computer Simulation of Biomolecules: Comparison with Experimental Data
in: Molecular Aspects of Biotechnology: Computational Models and Theories, J. Bertran, ed., NATO ASI Series C368, Kluwer Academic Publishers, Dordrecht, 1992, pp. 105-122

92.9
A.P. Heiner
Predictive Aspects of Molecular Dynamics Simulations for Proteins: Application to subtilisin BPN
Thesis, University of Groningen, August 1992

92.10
R.M. Sok, H.J.C. Berendsen and W.F. van Gunsteren
Molecular Dynamics Simulation of the Transport of Small Molecules across a Polymer Membrane
J. Chem. Phys. 96 (6) (1992) 4699-4704

92.11
K.E. Edgecombe, R.O. Esquivel, V.H. Smith, Jr. and F. Müller-Plathe
Pseudoatoms of the electron density
J. Chem. Phys. 97 (4) (1992) 2593-2599

92.12
W.F. van Gunsteren and A.E. Mark
Prediction of the Activity and Stability Effects of Site-directed Mutagenesis on a Protein Core
J. Mol. Biol. 227 (1992) 389-395

92.13
A.E. Mark and W.F. van Gunsteren
Simulation of the Thermal Denaturation of Hen Egg White Lysozyme: Trapping the Molten Globule State
Biochemistry 31 (34) (1992) 7745-7748

92.14
F. Müller-Plathe, S.C. Rogers and W.F. van Gunsteren
Computational Evidence for Anomalous Diffusion of Small Molecules in Amorphous Polymers
Chem. Phys. Letters 199 3,4 (1992) 237-243

92.15
M.A. Castro, S. Canuto and F. Müller-Plathe
Many-body-perturbation-theory calculations of the microwave and vibrational constants of CaC
Physical Review A 46, 7 (1992) 4415-4417, The American Physical Society, 1992.

92.16
H.J.C. Berendsen, B. Egberts, S.-J. Marrink and P. Ahlström
Molecular Dynamics Simulations of Phospholipid Membranes and their Interaction with Phospholipase A2
in: Membrane Proteins: Structures, Interactions and Models, A. Pullman et al. (eds.), Kluwer Academic Publishers, 1992, pp. 457-470

92.17
H.J.C. Berendsen
Rationale for using NMR to study water relations in foods and biological tissues
Trends in Food Science & Technology 3 (1992) 202-205

92.18
F. Müller-Plathe, S.C. Rogers and W.F. van Gunsteren
Diffusion Coefficients of Penetrant Gases in Polyisobutylene Can Be Calculated Correctly by Molecular Dynamics Simulations
Macromolecules 25 (1992) 6722-6724

92.19
A.P. Heiner, H.J.C. Berendsen and W.F. van Gunsteren
MD Simulation of Subtilisin BPN' in a Crystal Environment
Proteins 14 (1992) 451-464

92.20
A.E. Torda and W.F. van Gunsteren
Molecular Modeling Using Nuclear Magnetic Resonance Data
in: Reviews in Computational Chemistry, Volume III, K.B. Lipkowitz, D.B. Boyd eds., VCH Publishers, Inc. New York, 1992, pp. 143-172

92.21
A. Gunzinger, U. Müller, W. Scott, B. Bäumle, P. Kohler and W.F. van Gunsteren
Architecture and Realization of a Multi Signalprocessor System
IEEE Computer Society Press Reprint, Los Alamitos, 1992, pp. 327-340

92.22
F. Müller-Plathe, W. Scott and W.F. van Gunsteren
Molecular Dynamics on Supercomputers: Implementations and Applications
SPEEDUP Journal 6 (1992) 33-38

92.23
A. Gunzinger, U.A. Müller, W. Scott, B. Bäumle, P. Kohler, H.R. vonder Mühll, F. Müller-Plathe, W.F. van Gunsteren, W. Guggenbühl
Achieving Super Computer Performance with a DSP Array Processor
IEEE Computer Society Press Reprint, Los Alamitos, 1992, pp. 543-550

92.24
S.P. van Helden, B.P. van Eijck, A.E. Mark, W.F. van Gunsteren and L.H.M. Janssen
Molecular Dynamics and free energy perturbation calculations on complexes of alpha-cyclodextrins with p-substituted phenols. A comparison between experiment and simulation
In: "Minutes of the 6th International Symposium on Cyclodextrins", A.R. Hedges ed., Editions de Santé, Paris, (1992), pp. 170-175

1993

93.1
A.E. Torda, R.M. Brunne, T. Huber, H. Kessler and W.F. van Gunsteren
Structure refinement using time-averaged J-coupling constant restraints
J. Biomol. NMR 3 (1993) 55-66

93.2
P.M. King, R.M. Spycher and W.F. van Gunsteren
Structure elucidation from rotation spectra: a penalty function approach
Chem. Phys. Letters 203 (1993) 88-92

93.3
P.E. Smith, R.M. Brunne, A.E. Mark and W.F. van Gunsteren
Dielectric Properties of Trypsin Inhibitor and Lysozyme Calculated from Molecular Dynamics Simulations
J. Phys. Chem. 97 (1993) 2009-2014

93.4
W.F. van Gunsteren
Molecular dynamics studies of proteins
Current Opinion in Structural Biology 3 (1993) 277-281

93.5
W. Scott, A. Gunzinger, B. Bäumle, P. Kohler, U.A. Müller, H-R. Vonder Mühll, A. Eichenberger, W. Guggenbühl, N. Ironmonger, F. Müller-Plathe and W.F. van Gunsteren
Parallel molecular dynamics on a multi signalprocessor system
Computer Physics Communications 75 (1993) 65-86

93.6
A.H. Juffer
On the Modelling of Solvent Mean Force Potentials. From Liquid Argon to Solvated Macromolecules
Thesis, University of Groningen, April 1993

93.7
Shi Yun-yu, A.E. Mark, Wang Cun-xin, Huang Fuhua, H.J.C. Berendsen and W.F. van Gunsteren
Can the stability of protein mutants be predicted by free energy calculations ?
Protein Engineering 6 (1993) 289-295

93.8
S.T. Jones, P. Ahlström, H.J.C. Berendsen and R.W. Pickersgill
Molecular dynamics simulation of a phospholipase A2 - substrate complex
Biochimica et Biophysica Acta 1162 (1993) 135-142

93.9
K.E. Edgecombe, V.H. Smith, Jr. and F. Müller-Plathe
Nonnuclear Maxima in the Charge Density
Z. Naturforsch. 48a (1993) 127-133

93.10
R.M. Brunne and W.F. van Gunsteren
Dynamical properties of bovine pancreatic trypsin inhibitor from a molecular dynamics simulation at 5000 atm
FEBS Letters 323 (1993) 215-217

93.11
R.M. Brunne, W.F. van Gunsteren, R. Brüschweiler and R.R. Ernst
Molecular Dynamics Simulation of the Proline Conformational Equilibrium and Dynamics in Antamanide Using the GROMOS Force Field
J. Am. Chem. Soc. 115 (1993) 4764-4768

93.12
F. Müller-Plathe, S.C. Rogers and W.F. van Gunsteren
Gas sorption and transport in polyisobutylene: Equilibrium and nonequilibrium molecular dynamics simulations
J. Chem. Phys. 98 (1993) 9895-9904

93.13
T.S. Harvey and W.F. van Gunsteren
The Application of Chemical Shift Calculation to Protein Structure Determination by NMR Techniques in Protein Chemistry IV (1993), Academic Press, pp. 615-622

93.14
P.R. Gerber, A.E. Mark and W.F. van Gunsteren
An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes
J. Computer-Aided Molecular Design 7 (1993) 305-323

93.15
A.P. Heiner, H.J.C. Berendsen and W.F. van Gunsteren
Structure prediction of Subtilisin BPN' mutants using molecular dynamics methods
Protein Engineering 6 (1993) 397-408

93.16
A.H. Juffer and H.J.C. Berendsen
Dynamic surface boundary conditions. A simple boundary model for molecular dynamics simulations
Molecular Physics 79 (1993) 623-644

93.17
R.M. Brunne, E. Liepinsh, G. Otting, K. Wüthrich and W.F. van Gunsteren
Hydration of Proteins: A Comparison of Experimental Residence Times of Water Molecules Solvating the Bovine Pancreatic Trypsin Inhibitor with Theoretical Model Calculations
J. Mol. Biol. 231 (1993) 1040-1048

93.18
P. Gros and W.F. van Gunsteren
Crystallographic Refinement and Structure-Factor Time-Averaging by Molecular Dynamics in the Absence of a Physical Force Field
Molecular Simulation 10 (1993) 377-395

93.19
C.K. Kuhn and W.F. van Gunsteren
Dynamics of solitons in polyacetylene in the step-potential model
Solid State Commun. 87 (1993) 203-207

93.20
F. Müller-Plathe, L. Laaksonen and W.F. van Gunsteren
Cooperative effects in the transport of small molecules through an amorphous polymer matrix
J. Mol. Graphics 11 (1993) 118-126

93.21
A.R. van Buuren, S.-J. Marrink and H.J.C. Berendsen
A Molecular Dynamics Study of the Decane/Water Interface
J. Phys. Chem. 97 (1993) 9206-9212

93.22
P.E. Smith and W.F. van Gunsteren
The viscosity of SPC and SPC/E water at 277 and 300K
Chem. Phys. Letters 215 (1993) 315-318

93.23
A. Amadei, A.B.M. Linssen and H.J.C. Berendsen
Essential Dynamics of Proteins
Proteins 17 (1993) 412-425

93.24
S.-J. Marrink, M. Berkowitz and H.J.C. Berendsen
Molecular Dynamics Simulation of a Membrane/Water Interface: The Ordering of Water and Its Relation to the Hydration Force
Langmuir 9 (1993) 3122-3131

93.25
F. Müller-Plathe
YASP: A molecular simulation package
Comput. Phys. Commun. 78 (1993) 77-94

93.26
R.C. van Schaik, H.J.C. Berendsen, A.E. Torda and W.F. van Gunsteren
A Structure Refinement Method Based on Molecular Dynamics in Four Spatial Dimensions
J. Mol. Biol. 234 (1993) 751-762

93.27
N. El Tayar, A.E. Mark, P. Vallat, R.M. Brunne, B. Testa and W.F. van Gunsteren
Solvent-Dependent Conformation and Hydrogen-Bonding Capacity of Cyclosporin A: Evidence From Partition Coefficients and Molecular Dynamics Simulations
J Med. Chem. 36 (1993) 3757-3764

93.28
W.F. van Gunsteren
Molecular dynamics and stochastic dynamics simulation: A primer
In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", Vol. 2, W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson eds., Escom Science Publishers, Leiden, The Netherlands, (1993), pp. 3-36

93.29
W.F. van Gunsteren, T.C. Beutler, F. Fraternali, P.M. King, A.E. Mark and P.E. Smith
Computation of free energy in practice: choice of approximations and accuracy limiting factors
In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", Vol. 2, W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson eds., Escom Science Publishers, Leiden, The Netherlands, (1993), pp. 315-348

93.30
P.M. King
Free Energy via molecular simulation: A primer
In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", Vol. 2, W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson eds., Escom Science Publishers, Leiden, The Netherlands, (1993), pp. 267-314

93.31
P.E. Smith and W.F. van Gunsteren
Methods for the evaluation of long-range electrostatic forces in computer simulations of molecular systems
In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", Vol. 2, W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson eds., Escom Science Publishers, Leiden, The Netherlands, (1993), pp. 182-212

93.32
J. Mavri, H.J.C. Berendsen and W.F. van Gunsteren
Influence of Solvent on Intramolecular Proton Transfer in Hydrogen Malonate. Molecular Dynamics Simulation Study of Tunneling by Density Matrix Evolution and Nonequilibrium Solvation
J. Phys. Chem. 97 (1993) 13469-13476

93.33
P. Ahlström and H.J.C. Berendsen
A Molecular Dynamics Study of Lecithin Monolayers
J. Phys. Chem. 97 (1993) 13691-13702

93.34
H.J.C. Berendsen and J. Mavri
Quantum Simulation of Reaction Dynamics by Density Matrix Evolution
J. Phys. Chem. 97 (1993) 13464-13468

93.35
H.J.C. Berendsen
Electrostatic interactions
In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", Vol. 2, W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson eds., Escom Science Publishers, Leiden, The Netherlands, (1993), pp. 161-181

93.36
H.J.C. Berendsen and S.-J. Marrink
Molecular dynamics of water transport through membranes: Water from solvent to solute
Pure & Appl. Chem. 65 (1993) 2513-2520

93.37
H. Bekker, E.J. Dijkstra and H.J.C. Berendsen
Molecular Dynamics simulation on an i860 based ring architecture
Supercomputer 54 (1993) 4-10

93.38
A.R. van Buuren and H.J.C. Berendsen
Molecular Dynamics Simulation of the Stability of a 22-Residue Alpha-Helix in Water and 30% Trifluoroethanol
Biopolymers 33 (1993) 1159-1166

93.39
H. Bekker, H.J.C. Berendsen, E.J. Dijkstra, S. Achterop, R. v. Drunen, D. v.d. Spoel, A. Sijbers, H. Keegstra, B. Reitsma and M.K.R. Renardus
GROMACS: a Parallel Computer for Molecular Dynamics Simulations
In: Proceedings of the 4th Intl. Conference Physics Computing '92, R.A. de Groot and J. Nadrchal eds., World Scientific Publishing Company, Singapore, 1993, pp. 252-256

93.40
H. Bekker, H.J.C. Berendsen, E.J. Dijkstra, S. Achterop, R. v. Drunen, D. v.d. Spoel, A. Sijbers, H. Keegstra, B. Reitsma and M.K.R. Renardus
GROMACS Method of Virial Calculation Using a Single Sum
In: Proceedings of the 4th Intl. Conference Physics Computing '92, R.A. de Groot and J. Nadrchal eds., World Scientific Publishing Company, Singapore, 1993, pp. 257-261

1994

94.1
P.E. Smith and W.F. van Gunsteren
Predictions of free energy differences from a single simulation of the initial state
J. Chem. Phys. 100 (1994) 577-585

94.2
T.C. Beutler and W.F. van Gunsteren
The computation of a potential of mean force: Choice of the biasing potential in the umbrella sampling technique
J. Chem. Phys. 100 (1994) 1492-1497

94.3
R.C. van Schaik
Novel Search Algorithms for Biomolecular Structure Refinement
Thesis, University of Groningen, March 1994

94.4
E. Egberts, S.-J. Marrink and H.J.C. Berendsen
Molecular dynamics simulation of a phospholipid membrane
Eur. Biophys. J. 22 (1994) 423-436

94.5
P.E. Smith and W.F. van Gunsteren
Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K
J. Chem. Phys. 100 (1994) 3169-3174

94.6
P.E. Smith and W.F. van Gunsteren
Translational and Rotational Diffusion of Proteins
J. Mol. Biol. 236 (1994) 629-636

94.7
R. Leenders, W.F. van Gunsteren, H.J.C. Berendsen and A.J.W.G. Visser
Molecular Dynamics Simulations of Oxidized and Reduced Clostridium beijerinckii Flavodoxin
Biophysical Journal 66 (1994) 634-645

94.8
X. de la Cruz, A.E. Mark, J. Tormo, I. Fita and W.F. van Gunsteren
Investigation of Shape Variations in the Antibody Binding Site by Molecular Dynamics Computer Simulation
J. Mol. Biol. 236 (1994) 1186-1195

94.9
S.R. Billeter, P.M. King and W.F. van Gunsteren
Can the density maximum of water be found by computer simulation ?
J. Chem. Phys. 100 (1994) 6692-6699

94.10
F. Fraternali and W.F. van Gunsteren
Conformational Transitions of a Dipeptide in Water: Effects of Imposed Pathways Using Umbrella Sampling Techniques
Biopolymers 34 (1994) 347-355

94.11
T. Mordasini Denti, W.F. van Gunsteren and F. Diederich
Studies toward computer liquid phase simulations of the solvent-dependency of apolar association strength: conformational analysis of a cyclophane-pyrene complex by pseudo Monte Carlo and molecular dynamics methods
In: "Computational Approaches in Supramolecular Chemistry", G. Wipff ed., Kluwer Academic Publishers, The Netherlands, (1994), pp. 11-136

94.12
T.C. Beutler, A.E. Mark, R.C. van Schaik, P.R. Gerber and W.F. van Gunsteren
Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
Chem. Phys. Letters 222 (1994) 529-539

94.13
N.A.J. van Nuland, I.W. Hangyi, R.C. van Schaik, H.J.C. Berendsen, W.F. van Gunsteren, R.M. Scheek and G.T. Robillard
The High-resolution Structure of the Histidine-containing Phosphocarrier Protein HPr from Escherichia coli Determined by Restrained Molecular Dynamics from Nuclear Magnetic Resonance Nuclear Overhauser Effect Data
J. Mol. Biol. 237 (1994) 544-559

94.14
W.F. van Gunsteren, F.J. Luque, D. Timms and A.E. Torda
MOLECULAR MECHANICS IN BIOLOGY: From Structure to Function, Taking Account of Solvation
Ann. Rev. Biophys. Biomol. Structure 23 (1994) 847-863

94.15
A.E. Mark and W.F. van Gunsteren
Decomposition of the Free Energy of a System in Terms of Specific Interactions: Implications for Theoretical and Experimental Studies
J. Mol. Biol. 240 (1994) 167-176

94.16
A.E. Mark, S.P. van Helden, P.E. Smith, L.H.M. Janssen and W.F. van Gunsteren
Convergence Properties of Free Energy Calculations: Alpha-Cyclodextrin Complexes as a Case Study
J. Am. Chem. Soc. 116 (1994) 6293-6302

94.17
A.A. Gusev, F. Müller-Plathe, W.F. van Gunsteren and U.W. Suter
Dynamics of Small Molecules in Bulk Polymers
Adv. Polym. Sci. 116 (1994) 207-247

94.18
T.C. Beutler and W.F. van Gunsteren
Molecular dynamics free energy calculation in four dimensions
J. Chem. Phys. 101 (1994) 1417-1422

94.19
W. Scott. F. Müller-Plathe and W.F. van Gunsteren
Molecular dynamics study of the mixing and demixing of a binary Lennard-Jones fluid
Molecular Physics 82 (1994) 1049-1062

94.20
F. Müller-Plathe
Permeation of polymers: A computational approach
Acta Polymer 45 (1994) 259-293

94.21
J. Mavri and H.J.C. Berendsen
Dynamical simulation of a quantum harmonic oscillator in a noble-gas bath by density-matrix evolution
Phys. Rev. E, 50 (1994) 198-204

94.22
A.R. van Buuren and H.J.C. Berendsen
Molecular Dynamics Simulations of Carbohydrate-Based Surfactants in Surfactant/Water/Oil Systems
Langmuir 10 (1994) 1703-1713

94.23
A.R. van Buuren and H.J.C. Berendsen
Molecular Dynamics Simulations of Molecular Systems
in: "Crossing Over in Chemistry", A.R. van Buuren ed., Proceedings of the 2nd Annual Advanced Research Workshop, 15-17 January 1994, Eischoll, Switzerland

94.24
S.-J. Marrink and H.J.C. Berendsen
Simulation of Water Transport through a Lipid Membrane
J. Phys. Chem. 98 (1994) 4155-4168

94.25
J. Mavri and H.J.C. Berendsen
Treatment of nonadiabatic transitions by density matrix evolution and molecular dynamics simulations
J. Molecular Structure 322 (1994) 1-7

94.26
W.F. van Gunsteren, R.M. Brunne, P. Gros, R.C. van Schaik, C.A. Schiffer and A.E. Torda
Accounting for Molecular Mobility in Structure Determination Based on Nuclear Magnetic Resonance Spectroscopic and X-Ray Diffraction Data
in: "Methods in Enzymology: Nuclear Magnetic Resonance", Vol. 239, T.L. James, N.J. Oppenheimer eds., Academic Press, New York, (1994), pp. 619-654

94.27
C.A. Schiffer, R. Huber, K. Wüthrich and W.F. van Gunsteren
Simultaneous Refinement of the Structure of BPTI Against NMR Data Measured in Solution and X-ray Diffraction Data Measured in Single Crystals
J. Mol. Biol. 241 (1994) 588-599

94.28
F. Müller-Plathe and W.F. van Gunsteren
Can Simple Quantum-Chemical Continuum Models Explain the Gauche Effect in Poly(ethylene oxide)?
Macromolecules 27 (1994) 6040-6045

94.29
A.E. Torda and W.F. van Gunsteren
Algorithms For Clustering Molecular Dynamics Configurations
J. Comput. Chem. 15 (1994) 1331-1340

94.30
A.P. Nanzer, F.M. Poulsen, W.F. van Gunsteren and A.E. Torda
A Reassessment of the Structure of Chymotrypsin Inhibitor 2 (CI-2) Using Time-Averaged NMR restraints
Biochemistry 33 (1994) 14503-14511

94.31
A. Di Nola, D. Roccatano and H.J.C. Berendsen
Molecular Dynamics simulation of the docking of substrates to proteins
Proteins 19 (1994) 174-182

94.32
S.J. Marrink
Permeation of Small Molecules Across Lipid Membranes
Thesis, University of Groningen, November 1994

94.33
M. Yoneya and H.J.C. Berendsen
Molecular Dynamics Simulations of Chiral Nematic Liquid Crystals
J. Phys. Soc. Japan 63 (1994) 1025-1030

94.34
J. Mavri, M. Lensink and H.J.C. Berendsen
Treatment of inelastic collisions of a particle with a quantum harmonic oscillator by density matrix evolution
Molecular Physics 82 (1994) 1249-1257

94.35
F. Müller-Plathe, W. Scott and W.F. van Gunsteren
PARALLACS: A benchmark for parallel molecular dynamics
Computer Physics Communications 84 (1994) 102-114

94.36
I.G. Tironi and W.F. van Gunsteren
A molecular dynamics simulation study of chloroform
Molecular Physics 83 (1994) 381-403

94.37
R.M. Sok
Permeation of Small Molecules across a Polymer Membrane: a Computer Simulation Study
Thesis, University of Groningen, November 1994

94.38
T. Huber, A.E. Torda and W.F. van Gunsteren
Local elevation: A method for improving the searching properties of molecular dynamics simulation
J. Comput.-Aided Mol. Design 8 (1994) 695-708

94.39
H. Bekker and P. Ahlström
The Virial of Angle Dependent Potentials in Molecular Dynamics Simulations
Molecular Simulation 13 (1994) 367-374

94.40
M. Yoneya, H.J.C. Berendsen and K. Hirasawa
A Non-Iterative Matrix Method for Constraint Molecular Dynamics Simulations
Molecular Simulation 13 (1994) 395-405

94.41
P.E. Smith and W.F. van Gunsteren
When are Free Energy Components Meaningful?
J. Phys. Chem. 98 (1994) 13735-13740

94.42
T.C. Beutler
Thermodynamic properties derived from molecular dynamics computer simulations: Improved methods for the application to biomolecular systems
Thesis, ETH Zürich, December 1994

94.43
T.C. Beutler and W.F. van Gunsteren
Molecular dynamics simulations with first order coupling to a bath of constant chemical potential
Molecular Simulation 14 (1994) 21-34

94.44
B.A. Luty, M.E. Davis, I.G. Tironi and W.F. van Gunsteren
A Comparison of Particle-Particle Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems
Molecular Simulation 14 (1994) 11-20

94.45
F. Müller-Plathe
How good are molecular local-density methods? Case studies: The quadrupole moment of benzene, geometry and electrostatics of dimethyl sulfoxide, and the conformations of dimethoxy ethane
Brazilian Journal of Physics 24 (1994) 965-976

94.46
W.F. van Gunsteren, P.M. King and A.E. Mark
Fundamentals of drug design from a biophysical viewpoint
Quart. Rev. Biophysics 27 (1994) 435-481

94.47
P. Ulrich, W. Scott, W.F. van Gunsteren and A.E. Torda
Newtonian Dynamics in Unusual Places: Parameterising a Low Resolution Force Field
In: "Annual Report 1993/1994 of the Competence Center for Computational Chemistry", F. Müller-Plathe and W. Korosec eds., ETH Zürich, Zürich, Switzerland (1994) pp. 17-25

1995

95.1
K. Esselink
Large-Scale Simulations of Many-Particles Systems
Thesis, University of Groningen, January 1995

95.2
C.A. Schiffer, P. Gros and W.F. van Gunsteren
Time-Averaging Crystallographic Refinement: Possibilities and Limitations Using Alpha-Cyclodextrin as a Test System
Acta Cryst. D51 (1995) 85-92

95.3
C.D. Berweger, W.F. van Gunsteren and F. Müller-Plathe
Force field parametrisation by weak coupling. Re-engineering SPC water
Chem. Phys. Letters 232 (1995) 429-436

95.4
H. Liu, F. Müller-Plathe and W.F. van Gunsteren
A molecular dynamics simulation study with a combined quantum mechanical and molecular mechanical potential energy function: Solvation effects on the conformational equilibrium of dimethoxyethane
J. Chem. Phys. 102 (1995) 1722-1730

95.5
P.E. Smith, R.C. van Schaik, T. Szyperski, K. Wüthrich and W.F. van Gunsteren
Internal Mobility of the Basic Pancreatic Trypsin Inhibitor in Solution: A Comparison of NMR Spin Relaxation Measurements and Molecular Dynamics Simulations
J. Mol. Biol. 246 (1995) 356-365

95.6
T.C. Beutler, D.R. Béguelin and W.F. van Gunsteren
Free energy of cavity formation in solvent: Computational, methodological and physical aspects
J. Chem. Phys. 102 (1995) 3787-3793

95.7
P.H. Hünenberger, A.E. Mark and W.F. van Gunsteren
Computational Approaches to Study Protein Unfolding: Hen Egg White Lysozyme as a Case Study
Proteins 21 (1995) 196-213

95.8
A.E. Mark and W.F. van Gunsteren
Free Energy Calculations in Drug Design: A Practical Guide
In: "New Perspectives in Drug Design", Proceedings of the 9th Intl. Roundtable,11-13 April 1994, Turnberry, Scotland, P.M. Dean, G. Jolles, C.G. Newton eds., Academic Press Ltd, (1995), pp. 185-200

95.9
H. Kovacs, A.E. Mark, J. Johansson and W.F. van Gunsteren
The Effect of Environment on the Stability of an Integral Membrane Helix: Molecular Dynamics Simulations of Surfactant Protein C in Chloroform, Methanol and Water
J. Mol. Biol. 247 (1995) 808-822

95.10
H. Bekker, H.J.C. Berendsen and W.F. van Gunsteren
Force and virial of torsional-angle dependent potentials
J. Comput. Chem. 16 (1995) 527-533

95.11
H. Bekker, E.J. Dijkstra, H.J.C. Berendsen and M.K.R. Renardus
An efficient, box shape independent non-bonded force and virial algorithm for Molecular Dynamics
Molecular Simulation 14 (1995) 137-151

95.12
H. Liu, F. Müller-Plathe and W.F. van Gunsteren
A Force Field for Liquid Dimethyl Sulfoxide and Physical Properties of Liquid Dimethyl Sulfoxide Calculated Using Molecular Dynamics Simulation
J. Am. Chem. Soc. 117 (1995) 4363-4366

95.13
W.F. van Gunsteren, P.H. Hünenberger, H. Kovacs, A.E. Mark and C.A. Schiffer
Investigation of protein unfolding and stability by computer simulation
Phil. Trans. R. Soc. Lond. B 348 (1995) 49-59

95.14
S.L. Njo, W.F. van Gunsteren and F. Müller-Plathe
Determination of force field parameters for molecular simulation by molecular simulation: An application of the weak-coupling method
J. Chem. Phys. 102 (1995) 6199-6207

95.15
I.G. Tironi, R. Sperb, P.E. Smith and W.F. van Gunsteren
A generalized reaction field method for molecular dynamics simulations
J. Chem. Phys. 102 (1995) 5451-5459

95.16
T.C. Beutler and W.F. van Gunsteren
Umbrella sampling along linear combinations of generalized coordinates
Theory and application to a glycine dipeptide
Chem. Phys. Letters 237 (1995) 308-316

95.17
P. Ahlström, J. Lausmaa, P. Löfgren and H.J.C. Berensen
Biomolecules and Phase Bounderies
Kluwer Academic Publishers, The Netherlands, (1995), pp. 371-379

95.18
S.-J. Marrink and M. Berkowitz
Water and Membranes
In: "Permeability and stability of lipid bilayers", E. Anibal Disalvo and S.A. Simon eds., CRC Press, Inc., (1995), pp. 21-48

95.19
D. van der Spoel and H.J.C. Berensen
MD simulation, Section 6.5
In: "Aspects of computational science", A.J. van der Steen ed., Stichting Nationale Computer Fac.,
s-Gravenhage, The Netherlands, (1995), pp. 367-378

95.20
A.R. van Buuren
Characterization of Oil/Water Interfaces:A Molecular Dynamics Study
Thesis, University of Groningen, September 1995

95.21
P.C. Jordan, P.J. van Maaren, J. Mavri, D. van der Spoel and H.J.C. Berendsen
Towards phase transferable potential functions: Methodology and application to nitrogen
J. Chem. Phys. 103 (1995) 2272-2285

95.22
C. Bisang, C. Weber, J. Inglis, C.A. Schiffer, W.F. van Gunsteren, I. Jelesarov, H.R. Bosshard and J.A. Robinson
Stabilization of Type-I ß-Turn Conformations in Peptides Containing the NPNA-Repeat Motif of the Plasmodium falciparum Circumsporozoite Protein by Substituting Proline for (S)-Alpha-Methylproline
J. Am. Chem. Soc. 117 (1995) 7904-7915

95.23
L.J. Smith, A.E. Mark, C.M. Dobson and W.F. van Gunsteren
Comparison of MD simulations and NMR experiments for hen lysozyme: Analysis of local fluctuations, cooperative motions and global changes
Biochemistry 34 (1995) 10918-10931

95.24
B.A. Luty, I.G. Tironi and W.F. van Gunsteren
Lattice-sum Methods for Calculating Electrostatic Interactions in Molecular Simulations
J. Chem. Phys. 103 (1995) 3014-3021

95.25
W.F. van Gunsteren, T. Huber and A.E. Torda
Biomolecular Modelling: Overview of Types of Methods to Search and Sample Conformational Space
European Conference on Computational Chemistry (E.C.C.C 1), American Institute of Physics, Conference Proceedings 330 (1995) 253-268

95.26
R.M. Brunne, K.D. Berndt, P. Güntert, K. Wüthrich and W.F. van Gunsteren
Structure and Internal Dynamics of the Bovine Pancreatic Trypsin Inhibitor in Aqueous Solution from Long-time Molecular Dynamics Simulations
Proteins 23 (1995) 49-62

95.27
J. Fennen, A.E. Torda and W.F. van Gunsteren
Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble
J. Biomol. NMR 6 (1995) 163-170

95.28
F. Müller-Plathe
Unexpected diffusion behaviour of gas molecules in crystalline poly(4-methyl-1-pentene)
J. Chem. Phys. 103 (1995) 4346-4351

95.29
W.F. van Gunsteren, P.H. Hünenberger, A.E. Mark, P.E. Smith and I.G. Tironi
Computer simulation of protein motion
Computer Phys. Communications 91 (1995) 305-319

95.30
F. Müller-Plathe, H. Liu and W.F. van Gunsteren
Conceptual Hierarchies in Polymer Electrolyte Simulations - From Quantum Chemistry to Molecular Dynamics
Comput. Polymer Science 5 (1995) 89-98

95.31
P.E. Smith and W.F. van Gunsteren
Reaction field effects on the simulated properties of liquid water
Molecular Simulation 15 (1995) 233-245

95.32
P.H. Hünenberger, A.E. Mark and W.F. van Gunsteren
Fluctuation and Cross-Correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations
J. Mol. Biol. 252 (1995) 492-503

95.33
A.P. Nanzer, W.F. van Gunsteren and A.E. Torda
Parametrisation of time-averaged distance restraints in MD simulations
J. Biomol. NMR 6 (1995) 313-320

95.34
F. Müller-Plathe and W.F. van Gunsteren
Computer simulation of a polymer electrolyte: Lithium iodide in amorphous poly(ethylene oxide)
J. Chem. Phys. 103 (1995) 4745-4756

95.35
W.R.P. Scott and W.F. van Gunsteren
The GROMOS software package for biomolecular simulations
In: "Methods and Techniques in Computational Chemistry: METECC-95", E. Clementi and G. Corongiu eds., STEF, Cagliari, Italy (1995), pp. 397-434

95.36
D.G. Green, K.E. Meecham, M. Surridge, F. van Hoesel and H.J.C. Berendsen
Parallelization of molecular dynamics code. GROMOS87 parallelization for distributed memory architectures
In: "Methods and Techniques in Computational Chemistry: METECC-95", E. Clementi and G. Corongiu eds., STEF, Cagliari, Italy (1995), pp. 435-463

95.37
A.R. van Buuren, S.J. Marrink and H.J.C. Berendsen
Characterisation of aqueous interfaces with different hydrophobicities by molecular dynamics
Colloids and Surfaces 102 (1995) 143-157

95.38
J. Mavri and H.J.C. Berendsen
Calculation of the Proton Transfer Rate Using Density Matrix Evolution and Molecular Dynamics Simulations: Inclusion of the Proton Excited States
J. Phys. Chem. 99 (1995) 12711-12717

95.39
D.M.F. van Aalten, A. Amadei, A.B.M. Linssen, V.G.H. Eijsink, G. Vriend and H.J.C. Berendsen
The Essential Dynamics of Thermolysin: Confirmation of the Hinge-Bending Motion and Comparison of Simulations in Vacuum and Water
Proteins 22 (1995) 45-54

95.40
H.J.C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Computer Phys. Communications 91 (1995) 43-56

95.41
A.R. van Buuren, J. de Vlieg and H.J.C. Berendsen
Structural Properties of 1,2-Diacyl-sn-glycerol in Bulk and at the Water Interface by Molecular Dynamics
Langmuir 11 (1995) 2957-2965

95.42
A. Amadei, A.B.M. Linssen, B.L. de Groot and H.J.C. Berendsen
Essential Degrees of Freedom of Proteins
In: "Modelling of Biomolecular Structures and Mechanisms", A. Pullman et al. eds., Kluwer Academic Publishers, The Netherlands, (1995), pp. 85-93

95.43
C.A. Schiffer, V. Dötsch, K. Wüthrich and W.F. van Gunsteren
Exploring the Role of the Solvent in the Denaturation of a Protein: A Molecular Dynamics Study of the DNA Binding Domain of the 434 Repressor
Biochemistry 34 (1995) 15057-15067

95.44
S.R. Billeter and W.F. van Gunsteren
A comparison of different numerical propagation schemes for solving the time-dependent Schrödinger equation in the position representation
Molecular Simulation 15 (1995) 301-322

95.45
A.E. Mark, Y. Xu, H. Liu and W.F. van Gunsteren
Rapid non-empirical approaches for estimating relative binding free energies
Acta Biochim. Polonica 42 (1995) 525-536

95.46
D. van der Spoel and H.J.C. Berendsen
Determination of proton transfer rate constants using ab initio, molecular dynamics and density matrix evolution calculations
In: "Pacific Symposium of Bio-Computing", World Scientific Singapore (1995) 624-637

95.47
D.M.F. van Aalten, J.B.C. Findlay, A. Amadei and H.J.C. Berendsen
Essential dynamics of the cellular retinol-binding protein - evidence for ligand-induced conformational changes
Protein Eng. 8 (1995) 1129-1135

1996

96.1
H. Liu, F. Müller-Plathe and W.F. van Gunsteren
Molecular Dynamics with a Quantum-Chemical Potential: Solvent Effects on an SN2 Reaction at Nitrogen
Chem. Eur. J. 2 (1996) 191-195

96.2
H.J.C. Berendsen and J. Mavri
Quantum dynamics simulation of a small quantum system embedded in a classical environment
In: "Quantum Mechanical Simulation Methods for Studying Biological Systems", Proceedings of Les Houches Workshop, 2-7 May, 1995, Les Houches, France, D. Bicout and M. Field eds., Springer-Verlag and Les Editions de Physique Les Ulis, France, (1996), pp. 157-179

96.3
A. Amadei, M.E.F. Apol, A. Di Nola and H.J.C. Berendsen
The quasi-Gaussian entropy theory: Free energy calculations based on the potential energy distribution function
J. Chem. Phys. 104 (1996) 1560-1574

96.4
B.A. Luty and W.F. van Gunsteren
Calculating Electrostatic Interactions Using the Particle-Particle Particle-Mesh Method with Nonperiodic Long-Range Interactions
J. Phys. Chem. 100 (1996) 2581-2587

96.5
T.C. Beutler, T. Bremi, R.R. Ernst and W.F. van Gunsteren
Motion and Conformation of Side Chains in Peptides. A Comparison of 2D Umbrella-Sampling Molecular Dynamics and NMR Results
J. Phys. Chem. 100 (1996) 2637-2645

96.6
F. Müller-Plathe
Simulation grosser Systeme. Trendbericht Theoretische Chemie 1996
Nachr. Chem. Techn. Lab. 44 (1996) 188-190

96.7
I.G. Tironi, R.M. Brunne and W.F. van Gunsteren
On the relative merits of flexible versus rigid models for use in computer simulations of molecular liquids
Chem. Phys. Letters 250 (1996) 19-24

96.8
F. Fraternali and W.F. van Gunsteren
An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution
J. Mol. Biol. 256 (1996) 939-948

96.9
J.J. Lopéz Cascales, J. Garcia de la Torre, S.J. Marrink and H.J.C. Berendsen
Molecular dynamics simulation of a charged biological membrane
J. Chem. Phys. 104 (1996) 2713-2720

96.10
T.Z. Mordasini Denti, T.C. Beutler, W.F. van Gunsteren and F. Diederich
Computation of Gibbs Free Energies of Hydration for Simple Aromatic Molecules: A Comparative Study Using Monte Carlo and Molecular Dynamics Computer Simulation Techniques
J. Phys. Chem. 100 (1996) 4256-4260

96.11
F. Müller-Plathe
Solvent dynamics in swollen polymers
Chem. Phys. Letters 252 (1996) 419-424

96.12
M.E.F. Apol, A. Amadei and H.J.C. Berendsen
Application of the quasi-Gaussian entropy theory to the calculation of thermodynamic properties of water and methane in the liquid and gas phase
J. Chem. Phys. 104 (1996) 6665-6678

96.13
H. Bekker
Molecular Dynamics Simulation Methods Revised
Thesis, University of Groningen, June 1996

96.14
W.F. van Gunsteren, A.P. Nanzer and A.E. Torda
Molecular simulation methods for generating ensembles or trajectories consistent with experimental data
In: "Monte Carlo and Molecular Dynamics of Condensed Matter Systems", Proceedings of the Eurofonference, 3-28 July 1995, Como, Italy, Vol. 49, K. Binder and G. Ciccotti eds., SIF, Bologna, Italy, (1996), pp. 777-788

96.15
H. Liu, A.E. Mark and W.F. van Gunsteren
Estimating the Relative Free Energy of Different Molecular States with Respect to a Single Reference State
J. Phys. Chem. 100 (1996) 9485-9494

96.16
H.J.C. Berendsen and J. Mavri
Approach to Nonadiabatic Transitions by Density Matrix Evolution and Molecular Dynamics Simulations
Int. J. Quantum Chem. 57 (1996) 965-983

96.17
D. van der Spoel, H.J. Vogel and H.J.C. Berendsen
Molecular Dynamics Simulations of N-Terminal Peptides From a Nucleotide Binding Protein
Proteins 24 (1996) 450-466

96.18
A.R. van Buuren, D.P. Tieleman, J. de Vlieg and H.J.C. Berendsen
Cosurfactants Lower Surface Tension of the Diglyceride/Water Interface: A Molecular Dynamics Study
Langmuir 12 (1996) 2570-2579

96.19
H.J.C. Berendsen
Bio-Molecular Dynamics Comes of Age
Science 271 (1996) 954-955

96.20
A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and H.J.C. Berendsen
An Efficient Method for Sampling the Essential Subspace of Proteins
J. Biomol. Structure & Dynamics 13 (1996) 615-625

96.21
B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen
Towards an Exhaustive Sampling of the Configurational Spaces of the Two Forms of the Peptide Hormone Guanylin
J. Biomol. Structure & Dynamics 13 (1996) 741-751

96.22
S.J. Marrink, R.M. Sok and H.J.C. Berendsen
Free volume properties of a simulated lipid membrane
J. Chem. Phys. 104 (1996) 9090-9099

96.23
J.J. Lopéz Cascales, H.J.C. Berendsen and J. Garcia de la Torre
Molecular Dynamics Simulation of Water between Two Charged Layers of Dipalmitoyl-phosphatidylserine
J. Phys. Chem. 100 (1996) 8621-8627

96.24
T.Z. Mordasini Denti, W.F. van Gunsteren and F. Diederich
Computer Simulations of the Solvent Dependence of Apolar Association Strength: Gibbs Free Energy Calculations on a Cyclophane-Pyrene Complex in Water and Chloroform
J. Am. Chem. Soc. 118 (1996) 6044-6051

96.25
F. Müller-Plathe
Local Structure and Dynamics in Solvent-Swollen Polymers
Macromolecules 29 (1996) 4782-4791

96.26
T. Huber, A.E. Torda and W.F. van Gunsteren
Optimization Methods for Conformational Sampling Using a Boltzmann-Weighted Mean Field Approach
Biopolymers 39 (1996) 103-114

96.27
X. Daura, P.H. Hünenberger, A.E. Mark, E. Querol, F.X. Avilés and W.F. van Gunsteren
Free Energies of Transfer of Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions
J. Am. Chem. Soc. 118 (1996) 6285-6294

96.28
H. Liu, F. Müller-Plathe and W.F. van Gunsteren
A Combined Quantum/Classical Molecular Dynamics Study of the Catalytic Mechanism of HIV-Protease
J. Mol. Biol. 261 (1996) 454-469

96.29
C.A. Schiffer and W.F. van Gunsteren
Structural Stability of Disulfide Mutants of Basic Pancreatic Trypsin Inhibitor: A Molecular Dynamics Study
Proteins 26 (1996) 66-71

96.30
M.E.F. Apol, A. Amadei and H.J.C. Berendsen
Derivation of a thermodynamic closure relation in the isothermal-isobaric ensemble using quasi-Gaussian entropy theory
Chem. Phys. Letters 256 (1996) 172-178

96.31
S.J. Marrink, F. Jähnig and H.J.C. Berendsen
Proton Transport across Transient Single-Fit Water Pores in a Lipid Membrane Studied by Molecular Dynamics Simulations
Biophys. J. 71 (1996) 632-647

96.32
F. Müller-Plathe
An All-atom Force Field for Liquid Ethanol - Properties of Ethanol-Water Mixtures
Molecular Simulation 18 (1996) 133-143

96.33
I.G. Tironi, P. Fontana and W.F. van Gunsteren
A molecular dynamics simulation study of liquid carbon tetrachloride
Mol. Simulation 18 (1996) 1-11

96.34
S.J. Marrink and H.J.C. Berendsen
Permeation Process of Small Molecules across Lipid Membranes Studied by Molecular Dynamics Simulations
J. Phys. Chem. 100 (1996) 16729-16738

96.35
D.P. Tieleman and H.J.C. Berendsen
Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters
J. Chem. Phys. 105 (1996) 4871-4880

96.36
B.L. de Groot, D.M.F. van Aalten, A. Amadei and H.J.C. Berendsen
The Consistency of Large Concerted Motions in Proteins in Molecular Dynamics Simulations
Biophysical Journal 71 (1996) 1707-1713

96.37
A. Amadei, D. Roccatano, M.E.F. Apol, H.J.C. Berendsen and A. Di Nola
Prediction of the liquid-vapor equilibrium pressure using the quasi-Gaussian entropy theory
J. Chem. Phys. 105 (1996) 7022-7025

96.38
D. van der Spoel, A.R. van Buuren, D.P. Tieleman and H.J.C. Berendsen
Molecular dynamics simulations of peptides from BPTI: A closer look at amide-aromatic interactions
J. Biomol. NMR 8 (1996) 229-238

96.39
A.P. Nanzer, T. Huber, A.E. Torda and W.F. van Gunsteren
Molecular dynamics simulation using weak-coupling NOE distance restraining
J. Biomol. NMR 8 (1996) 285-291

96.40
W.F. van Gunsteren, S.R. Billeter, A.A. Eising, P.H. Hünenberger, P. Krüger, A.E. Mark, W.R.P. Scott, I.G. Tironi
Biomolecular Simulation: The GROMOS96 Manual and User Guide
Vdf Hochschulverlag AG an der ETH Zürich, Zürich, Switzerland (1996) pp. 1-1042

96.41
P.R. Ulrich
Development of a novel protein structure prediction force field
Thesis, ETH Zürich, November 1996

96.42
J.W. Peng, C.A. Schiffer, P. Xu, W.F. van Gunsteren and R.R. Ernst
Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide
J. Biomol. NMR 8 (1996) 453-476

96.43
B.L. de Groot, A. Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen
An Extended Sampling of the Configurational Space of HPr from E. coli
Proteins 26 (1996) 314-322

96.44
D. van der Spoel, B.L. de Groot, S. Hayward, H.J.C. Berendsen and H.J. Vogel
Bending of the calmodulin central helix: A theoretical study
Protein Science 5 (1996) 2044-2053

96.45
D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen
Molecular Modeling of the RNA Binding N-Terminal Part of Cowpea Chlorotic Mottle Virus Coat Protein in Solution with Phosphate Ions
Biophys. J. 71 (1996) 2920-2932

96.46
D. van der Spoel
Structure and Dynamics of Peptides: Theoretical Aspects of Protein Folding
Thesis, University of Groningen, The Netherlands, December 1996

96.47
P. Lijnzaad, H.J.C. Berendsen and P. Argos
Hydrophobic Patches on the Surfaces of Protein Structures
Proteins 25 (1996) 389-397

96.48
P. Lijnzaad, H.J.C. Berendsen and P. Argos
A Method for Detecting Hydrophobic Patches on Protein Surfaces
Proteins 26 (1996) 192-203

96.49
A.P. Nanzer
Molecular dynamics simulations to determine structure and dynamics of biomolecules using nuclear magnetic resonance data
Thesis, ETH Zürich, July 1996

96.50
A.C. Bach, II, S.X. Tang, J.R. Espina, P.F.W. Stouten, W.F. deGrado, J. Fennen, A.E. Torda, A.P. Nanzer and W.F. van Gunsteren
Restrained molecular dynamics of RGD-containing cyclic peptides using time-averaged NOEs
In: "Peptides: Chemistry, Structure and Biology", Proceedings of the 14th American Peptide Symposium, 18-23 June 1995, Columbus, Ohio, USA, P.T.P. Kaumaya and R.S. Hodges eds., Mayflower Scientific Ltd., England, (1996) pp. 489-490

96.51
M.F. Lensink, J. Mavri and H.J.C. Berendsen
Simultaneous Integration of Mixed Quantum-Classical Systems by Density Matrix Evolution Equations Using Interaction Representation and Adaptive Time Step Integrator
J. Comp. Chem. 17 (1996) 1287-1295

96.52
D.M.F. van Aalten, A. Amadei, R. Bywater, J.B.C. Findlay, H.J.C. Berendsen, C. Sander and P.F.W. Stouten
A Comparison of Structural and Dynamic Properties of Different Simulation Methods Applied to SH3
Biophys. J. 70 (1996) 684-692

1997

97.1
I.G. Tironi
Treatment of electrostatic interactions in molecular systems: development of methodology and application to liquids
Thesis, ETH Zürich, January 1997

97.2
P.H. Hünenberger
Molecular dynamics simulations using empirical force fields: Principles and applications to selected systems of chemical and biochemical interest
Thesis, ETH Zürich, January 1997

97.3
A. Amadei, M.E.F. Apol and H.J.C. Berendsen
Extensions of the quasi-Gaussian entropy theory
J. Chem. Phys. 106 (1997) 1893-1912

97.4
F. Müller-Plathe
Combining quantum chemistry and molecular simulation
In: "Advances in Quantum Chemistry", Vol 28, P.O. Löwdin, J.R. Sabin and M.C. Zerner eds., Academic Press, New York (1997) pp. 81-87

97.5
P. Ulrich, W.R.P. Scott, W.F. van Gunsteren and A.E. Torda
Protein Structure Prediction Force Fields: Parametrization With Quasi-Newtonian Dynamics
Proteins 27 (1997) 367-384

97.6
H. Kovacs, A.E. Mark and W.F. van Gunsteren
Solvent Structure at a Hydrophobic Protein Surface
Proteins 27 (1997) 395-404

97.7
S. Hayward, A. Kitao and H.J.C. Berendsen
Model-Free Methods of Analyzing Domain Motions in Proteins From Simulation: A Comparison of Normal Mode Analysis and Molecular Dynamics Simulation of Lysozyme
Proteins 27 (1997) 425-437

97.8
A.P. Nanzer, A.E. Torda, C. Bisang, C. Weber, J.A. Robinson and W.F. van Gunsteren
Dynamical Studies of Peptide Motifs in the Plasmodium falciparum Circumsporozoite Surface Protein by Restrained and Unrestrained MD Simulations
J. Mol. Biol. 267 (1997) 1012-1025

97.9
I.G Tironi, B.A. Luty and W.F. van Gunsteren
Space-time correlated reaction field: A stochastic dynamical approach to the dielectric continuum
J. Chem. Phys. 106 (1997) 6068-6075

97.10
U. Röthlisberger and M. Parrinello
Ab initio molecular dynamics simulation of liquid hydrogen fluoride
J. Chem. Phys. 106 (1997) 4658-4664

97.11
F. Müller-Plathe and W.F. van Gunsteren
Solvation of poly(vinyl alcohol) in water, ethanol and an equimolar water-ethanol mixture: structure and dynamics studied by molecular dynamics simulation
Polymer 38 (1997) 2259-2268

97.12
T.L. Huber
Searching and sampling methods for biomolecular modelling
Thesis, ETH Zürich, May 1997

97.13
M. Sprik, U. Röthlisberger and M.L. Klein
Structure of Solid Poly(tetrafluoroethylene): A Computer Simulation Study of Chain Orientational, Translational, and Conformational Disorder
J. Phys. Chem. B 101 (1997) 2745-2749

97.14
D.M.F. van Aalten, B.L. de Groot, J.B.C. Findlay, H.J.C. Berendsen and A. Amadei
A Comparison of Techniques for Calculating Protein Essential Dynamics
J. Comp. Chem. 18 (1997) 169-181

97.15
D. van der Spoel and H.J.C. Berendsen
Molecular Dynamics Simulations of Leu-Enkephalin in Water and DMSO
Biophys. J. 72 (1997) 2032-2041

97.16
M.E.F. Apol
The Quasi-Gaussian Entropy Theory
Thesis, University of Groningen, June 1997

97.17
F.A. Hamprecht, W.R.P. Scott and W.F. van Gunsteren
Generation of Pseudonative Protein Structures for Threading
Proteins 28 (1997) 522-529

97.18
W.F. van Gunsteren and A.E. Mark
Computational Chemistry: Abschied vom Experiment?
ETH-Bulletin 266 (1997) 18-19

97.19
P.H. Hünenberger, J.K. Granwehr, J.-N. Aebischer, N. Ghoneim, E. Haselbach and W.F. van Gunsteren
Experimental and Theoretical Approach to Hydrogen-Bonded Diastereomeric Interactions in a Model Complex
J. Am. Chem. Soc. 119 (1997) 7533-7544

97.20
T. Huber, A.E. Torda and W.F. van Gunsteren
Structure Optimisation Combining Soft-Core Interaction Functions, the Diffusion Equation Method and Molecular Dynamics
J. Phys. Chem. 101 (1997) 5926-5930

97.21
X. Daura, W.F. van Gunsteren, D. Rigo, B. Jaun and D. Seebach
Studying the Stability of a Helical ß-Heptapeptide by Molecular Dynamics Simulations
Chemistry - a European Journal 3 (1997) 1410-1417

97.22
C.D. Berweger, W.F. van Gunsteren and F. Müller-Plathe
Finite Element Interpolation for Combined Classical/Quantum Mechanical Molecular Dynamics Simulations
J. Comput. Chemistry 18 (1997) 1484-1495

97.23
B. Hess, H. Bekker, H.J.C. Berendsen and J.G.E.M. Fraaije
LINCS: A Linear Contstraint Solver for Molecular Simulations
J Comput. Chem. 18 (1997) 1463-1472

97.24
T. Nezel, F. Müller-Plathe, M.D. Müller and H.R. Buser
Theoretical Considerations about chiral PCBs and their Methylthio and Methylsulfonyl Metabolites being possibly present as stable Enantiomers
Chemosphere 35 (1997) 1895-1906

97.25
P.H. Hünenberger and W.F. van Gunsteren
Empirical classical interaction functions for molecular simulation
In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", Vol. 3, W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson eds., Kluwer Academic Publishers, Dordrecht, The Netherlands, (1997), pp. 3-82

97.26
S.R. Billeter and W.F. van Gunsteren
A modular molecular dynamics/quantum dynamics program for non-adiabatic proton transfers in solution
Comp. Phys. Comm. 107 (1997) 61-91

97.27
B.L. de Groot, D.M.F. van Aalten, R.M. Scheek, A. Amadei, G. Vriend and H.J.C. Berendsen
Prediction of Protein Conformational Freedom From Distance Constraints
Proteins 29 (1997) 240-251

97.28
H.J.C. Berendsen and J. Mavri
Simulating Proton Transfer Processes: Quantum Dynamics Embedded in a Classical Environment
In: "Theoretical Treatmens of Hydrogen Bonding", D. Hadzi (ed.), John Wiley & Sons Ltd. (1997) pp. 119-141

97.29
K. Park and W.F. van Gunsteren
Parameter Optimization for Calculation of Proton Chemical Shift in Protein
J. of Korean Mag. Res. Soc. 1 (1997) 71-78

97.30
K. Park and W.F. van Gunsteren
Solution Structure of Bovine Pancreatic Trypsin Inhibitor using NMR Chemical Shift Restraints
J. of Korean Mag. Res. Soc. 1 (1997) 79-94

97.31
D.P. Tieleman, S.J. Marrink and H.J.C. Berendsen
A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems
Biochim. Biophys. Acta, Reviews on Membranes 1331 (1997) 235-270

97.32
D.M.F. Van Aalten, D.A. Conn, B.L. De Groot, H.J.C. Berendsen, J.B.C. Findlay and A. Amadei
Protein dynamics derived from clusters of crystal structures
Biophys. J. 73 (1997) 2891-2896

1998

98.1
W.R.P. Scott
Molecular Dynamics Simulation of Biomolecules. Software Engineering, Parallelisation and Methodology
Thesis, ETH Zürich, March 1998

98.2
X. Daura, A.E. Mark and W.F. van Gunsteren
Parametrization of Aliphatic CHn United Atoms of GROMOS96 Force Field
J. Comput. Chem. 19 (1998) 535-547

98.3
W.F. van Gunsteren and A.E. Mark
Validation of molecular dynamics simulation
J. Chem. Phys. 108 (1998) 6109-6116

98.4
P.H. Hünenberger and W.F. van Gunsteren
Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural and dielectric properties of liquid water
J. Chem. Phys. 108 (1998) 6117-6134

98.5
U. Röthlisberger, M. Sprik and M.L. Klein
Living polymers: Ab initio molecular dynamics study of the initiation step in the polymerization of isoprene induced by ethyl lithium
J. Chem. Soc., Faraday Trans. 94 (1998) 501-508

98.6
W.F. van Gunsteren, H. Liu and F. Müller-Plathe
The elucidation of enzymatic reaction mechanisms by computer simulation: Human Immunodeficiency Virus protease catalysis
J. Mol. Structure (Theochem) 432 (1998) 9-14

98.7
C.D. Berweger, W.F. van Gunsteren and F. Müller-Plathe
Molecular dynamics simulation with an ab initio potential energy function and finite element interpolation: The photoisomerization of cis-stilbene in solution
J. Chem. Phys. 108 (1998) 8773-8781

98.8
S.R. Billeter and W.F. van Gunsteren
Protonizable Water Model for Quantum Dynamical Simulations
J. Phys. Chem. A 102 (1998) 4669-4678

98.9
D. van der Spoel, P.J. van Maaren and H.J.C. Berendsen
A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field
J. Chem. Phys. 108 (1998) 10220-10230

98.10
T. Huber and W.F. van Gunsteren
SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics
J. Phys. Chem. A 102 (1998) 5937-5943

98.11
X. Daura, B. Jaun, D. Seebach, W.F. van Gunsteren and A.E. Mark
Reversible Peptide Folding in Solution by Molecular Dynamics Simulation
J. Mol. Biol. 280 (1998) 925-932

98.12
L.J. Smith, A.E. Mark, C.M. Dobson and W.F. van Gunsteren
Molecular Dynamics Simulations of Peptide Fragments from Hen Lysozyme: Insight into Non-native Protein Conformations
J. Mol. Biol. 280 (1998) 703-719

98.13
A.M.J.J. Bonvin, M. Sunnerhagen, G. Otting and W.F. van Gunsteren
Water Molecules in DNA Recognition II: A Molecular Dynamics View of the Structure and Hydration of the trp Operator
J. Mol. Biol. 282 (1998) 859-873

98.14
M. Sunnerhagen, V.P. Denisov, K. Venu, A.M.J.J. Bonvin, J. Carey, B. Halle and G. Otting
Water Molecules in DNA Recognition I: Hydration Lifetimes of trp Operator DNA in Solution Measured by NMR Spectroscopy
J. Mol. Biol. 282 (1998) 847-858

98.15
D. Roccatano, A. Amadei, M.E.F. Apol, A. Di Nola and H.J.C. Berendsen
Application of the quasi-Gaussian entropy theory to molecular dynamics simulations of Lennard-Jones fluids
J. Chem. Phys. 109 (1998) 6358-6363

98.16
S. Billeter
Quantum dynamical simulation of non-adiabatic proton transfers in aqueous solution: methodology, molecular models and applications
Thesis, ETH Zürich, July 1998

98.17
W.R.P. Scott, A.E. Mark and W.F. van Gunsteren
On using time-averaging restraints in molecular dynamics simulation
J. Biomol. NMR 12 (1998) 501-508

98.18
P. Tieleman
Theoretical studies of membrane models: Molecular dynamics of water, lipids and membrane proteins
Thesis, University of Groningen, December 1998

98.19
A. Mark
Free energy perturbation calculations
Encyclopaedia of Computational Chemistry 2 (1998) 1070-1083

98.20
W.F. van Gunsteren, X. Daura and A.E. Mark
GROMOS force field
Encyclopaedia of Computational Chemistry 2 (1998) 1211-1216

98.21
L.D. Creveld, A. Amadei, R.C. van Schaik, H.A.M. Pepermans, J. de Vlieg and H.J.C. Berendsen
Identification of Functional and Unfolding Motions of Cutinase as Obtained From Molecular Dynamics Computer Simulations
Proteins 33 (1998) 253-264

1999

99.1
P.H. Hünenberger and W.F. van Gunsteren
Empirical Classical Force Fields for Molecular Systems
In: "Potential Energy Surfaces", Proceedings of the Mariapfarr Workshop in Theoretical Chemistry, A.F Sax ed., Springer-Verlag Berlin, 1999, pp. 178-214

99.2
A.E. Mark, H. Schäfer, H. Liu and W.F. van Gunsteren
Estimating Relative Free Energies from a Single Simulation of the Initial State
In: "Computational Molecular Dynamics: Challenges, Methods, Ideas", Proceedings of the 2nd Intl. Symp. on Algorithms for Macromol. Mod., P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, R.D. Skeel (eds.), Springe-Verlag Berlin, 1999, pp. 149-162

99.3
X. Daura, K. Gademann, B. Jaun, D. Seebach, W.F. van Gunsteren and A.E. Mark
Peptide Folding: When Simulation Meets Experiment
Angew. Chemie Intl. Ed. 38 (1999) 236-240
(German verion is also available)

99.4
X. Daura, R. Suter and W.F. van Gunsteren
Validation of molecular simulation by comparison with experiment: Rotational reorientation of tryptophan in water
J. Chem. Phys. 110 (1999) 3049-3055

99.5
X. Daura, W.F. van Gunsteren and A.E. Mark
Folding-Unfolding Thermodynamics of a beta-Heptapeptide From Equilibrium Simulations
Proteins 34 (1999) 269-280

99.6
L.J. Smith, C.M. Dobson and W.F. van Gunsteren
Side-chain Conformational Disorder in a Molten Globule: Molecular Dynamics Simulations of the A-state of Human alfa-lactalbumin
J. Mol. Biol. 286 (1999) 1567-1580

99.7
R. Walser, A.E. Mark and W.F. van Gunsteren
On the validity of Stokes' law at the molecular level
Chem. Phys. Letters 303 (1999) 583-586

99.8
S. Portmann, J.M. Galbraith, H.F. Schaefer, G.E. Scuseria and H.P. Lüthi
Some new structures of C28
Chem. Phys. Letters 301 (1999) 98-104

99.9
W. Klopper and H.P. Lüthi
The MP2 limit correction applied to coupled cluster calculations of the electronic dissociation energies of the hydrogen fluoride and water dimers
Molecular Physics 96 (1999) 559-570

99.10
H.P. Lüthi and S. Portmann
Bringing Theory to the Classroom: Summer School in Computational Quantum Chemistry (CQCS-98)
Chimia 53 (1999) 41-42

99.11
W.R.P. Scott, P.H. Hünenberger, I.G. Tironi, A.E. Mark, S.R. Billeter, J. Fennen, A.E. Torda, T. Huber, P. Krüger and W.F. van Gunsteren
The GROMOS Biomolecular Simulation Program Package
J. Phys. Chem. A 103 (1999) 3596-3607

99.12
M.F. Lensink, J. Mavri and H.J.C. Berendsen
Simulation of Slow Reaction with Quantum Character: Neutral Hydrolysis of Carboxylic Ester
J. Comput. Chem. 20 (1999) 886-895

99.13
L.J. Smith, C.M. Dobson and W.F. van Gunsteren
Molecular Dynamics Simulations of Human Alpha-Lactalbumin. Changes to the Structural and Dynamical Properties of the Protein at Low pH
Proteins 36 (1999) 77-86

99.14
W.F. van Gunsteren, A.M.J.J. Bonvin, X. Daura and L.J. Smith
Aspects of Modeling Biomolecular Structure on the Basis of Spectroscopic or Diffraction Data
In "Structure Computation and Dynamics in Protein NMR", Biol. Magnetic Resonance Vol. 17, Krishna and Berliner eds., Plenum Publishers, New York, 1999, pp. 3-35

99.15
C.A. Schiffer and W.F. van Gunsteren
Accessibility and Order of Water Sites in and Around Proteins: A Crystallographic Time-Averaging Study
Proteins 36 (1999) 501-511

99.16
X. Daura, I. Antes, W.F. van Gunsteren, W. Thiel and A.E. Mark
The Effect of Motional Averaging on the Calculation of NMR-Derived Structural Properties
Proteins 36 (1999) 542-555

99.17
K.A. Feenstra, B. Hess and H.J.C. Berendsen
Improving Efficiency of Large Time-Scale Molecular Dynamics Simulations of Hydrogen-Rich Systems
J. Comput. Chem. 20 (1999) 786-798

99.18
D.P. Tieleman, M.S.P. Sansom and H.J.C. Berendsen
Alamethicin Helices in a Bilayer and in Solution: Molecular Dynamics Simulations
Biophys. J. 76 (1999) 40-49

99.19
B.L. de Groot, G. Vriend and H.J.C. Berendsen
Conformational Changes in the Chaperonin GroEL: New Insights Into the Allosteric Mechanism
J. Mol. Biol. 286 (1999) 1241-1249

99.20
A.Amadei, B.L. de Groot, M.-A. Ceruso, M. Paci, A. Di Nola and H.J.C. Berendsen
A Kinetic Model for the Internal Motions of Proteins: Diffusion Between Multiple Harmonic Wells
Proteins 35 (1999) 283-292

99.21
H.J.C. Berendsen
Molecular Dynamics Simulations: The Limits and Beyond
In: "Computational Molecular Dynamics: Challenges, Methods, Ideas", Proceedings of the 2nd Intl. Symp. on Algorithms for Macromol. Mod., P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, R.D. Skeel (eds.), Springer-Verlag Berlin, 1999, pp. 3-36

99.22
C.D. Berweger, W.F. van Gunsteren and F. Müller-Plathe
The Photoisomerization of cis-Stilbene Does not Follow the Minimum Energy Path
Angew. Chemie Intl. Edit. 38 (1999) 2609-2611
(German version is also available)

99.23
C.D. Berweger, W.F. van Gunsteren and F. Müller-Plathe
Viscosity Dependence and Solvent Effects in the Photoisomerisation of cis-Stilbene: Insight from a Molecular Dynamics Study with an ab initio Potential-Energy Function
J. Chem. Phys. 111 (1999) 8987-8999

99.24
H. Schäfer, W.F. van Gunsteren and A.E. Mark
Estimating Relative Free Energies from a Single Ensemble: Hydration Free Energies
J. Comput. Chem. 20 (1999) 1604-1617

99.25
X. Daura, A.E. Mark and W.F. van Gunsteren
Peptide folding simulations: No solvent required?
Comput. Phys. Commun. 123 (1999) 97-102

99.26
C.D. Berweger
Molecular Dynamics Simulations with a Quantum-Chemical Core: Methodology and Applications in Photochemistry and Bioinorganic Chemistry
Thesis, ETH ZÜrich, December 1999

99.27
P.H. Hünenberger, V. Helms, N. Narayana, S.S. Taylor and J.A. McCammon
Determinants of ligand binding to c-AMP dependent protein kinase
Biochemistry 38 (1999) 2358-2366

99.28
P.I.W. de Bakker, P.H. Hünenberger and J.A. McCammon
Molecular dynamics simulations of the hyperthermophilic protein Sac7d from Sulfolobus acidocaldaricus: Contribution of salt bridges to thermostability
J. Mol. Biol. 285 (1999) 1811-1830

99.29
P.H. Hünenberger and J.A. McCammon
Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: A continuum electrostatics study
J. Chem. Phys. 110 (1999) 1856-1872

99.30
P.H. Hünenberger and J.A. McCammon
Effect of artificial periodicity in simulation of biomolecules under Ewald boundary conditions: A continuum electrostatic study
Biophys. Chem. 78 (1999) 69-88

99.31
N.A. Baker, P.H. Hünenberger and J.A. McCammon
Polarization around an ion in a dielectric continuum with truncated electrostatic interactions
J. Chem. Phys. 110 (1999) 10679-10692

99.32
P.H. Hünenberger
Lattice-sum methods for computing electrostatic interactions in molecular simulations
In: "Simulation and theory of electrostatic interactions in solution: Computational chemistry, biophysics and aqueous solution", L.R. Pratt and G. Hummer eds., AIP, New York, 1999, pp. 17-83

99.33
P.F. Flükiger, S. Portmann and H.P. Lüthi
Synchronous Communication of Molecular and Electronic Structure Information in a Distributed Computing Environment
In: "Lecture Notes in Computer Science", 1615, High Performance Computing, Springer Verlag, 1999

99.34
S. Tsuzuki, W. Klopper and H.P. Lüthi
High-level ab initio computations of structures and relative energies of two isomers of the CO2 trimer
J. Chem. Phys. 111 (1999) 3846-3854

99.35
H.P. Lüthi and S. Portmann
Bringing Theory to the Classroom: Summer School in Computational Quantum Chemistry (CQCS-98)
Chimia 53 (1999) 41-42

99.36
D.P. Tieleman, H.J.C. Berendsen and M.S.P. Sansom
An alamethicin channel in a lipid bilayer: Molecular dynamics simulations
Biophys. J. 76 (1999) 1757-1769

99.37
D.P. Tieleman, H.J.C. Berendsen and M.S.P. Sansom
Surface binding of alamethicin stabilizes its helical structure: Molecular dynamics simulations
Biophys. J. 76 (1999) 3186-3191

99.38
P. Meulenhoff
Interfacial Action of Phospholipase A2: a molecular dynamics study
Thesis, University of Groningen, The Netherlands, October 1999

2000

00.1
D. Seebach, J.V. Schreiber, S. Abele, X. Daura and W. F. van Gunsteren
Structure and conformation of ß-oligopeptide derivatives with simple proteinogenic side-chains. Circular dichroism and molecular dynamics investigations
Helv. Chim. Acta 83 (2000) 34-57

00.2
A.M.J.J. Bonvin and W.F. van Gunsteren
ß-hairpin Stability and Folding: Molecular Dynamics Studies of the First ß-Hairpin of Tendamistat
J. Mol. Biol. 296 (2000) 255-268

00.3
M.J. Mayor-López, J. Weber, H.P. Lüthi and K. Hegetschweiler
SCO trimers as high-energy materials? A density functional study
J. Mol. Model. 6 (2000) 55-64

00.4
C.W. Jefford, M. Grigorov, J. Weber, H.P. Lüthi and J.M.J. Tronchet
Correlating the molecular electrostatic potentials of some organic peroxides with their antimalarial activities
J. Chem. Inf. Comput. Sci. 40 (2000) 354-357

00.5
S.R. Billeter and W.F. van Gunsteren
Computer simulation of proton transfers of small acids in water
J. Phys. Chem. A 104 (2000) 3276-3286

00.6
W. Weber, P.H. Hünenberger and J.A. McCammon
Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation
J. Phys. Chem. B 104 (2000) 3668-3675

00.7
U. Stocker
Computer Simulation of Biomolecules: Investigation of Molecular Environment and Simulation Parameters
Thesis no 13686, ETH Zürich, May 2000

00.8
W. Damm and W.F. van Gunsteren
Reversible Peptide Folding: Dependence on the Molecular Force Field Used
J. Comput. Chem. 21 (2000) 774-787

00.9
R. Walser, A.E. Mark, W.F. van Gunsteren, M. Lauterbach and G. Wipff
The effect of force-field parameters on properties of liquids: Parametrization of a simple three-site model for methanol
J. Chem. Phys. 112 (2000) 10450-10459

00.10
U. Stocker and W.F. van Gunsteren
Molecular Dynamics Simulation of Hen Egg White Lysozyme: A Test of the GROMOS96 Force Field Against Nuclear Magnetic Resonance Data
Proteins 40 (2000) 145-153

00.11
X. Daura, E. Haaksma and W.F. van Gunsteren
Factor Xa: Simulation studies with an eye to inhibitor design
J. Comput.-Aided Mol. Design 14 (2000) 507-529

00.12
R. Walser, A.E. Mark and W.F. van Gunsteren
On the Temperature and Pressure Dependence of a Range of Properties of a Type of Water Model Commonly Used in High-Temperature Protein Unfolding Simulations
Biophys. J. 78 (2000) 2752-2760

00.13
D.P. Tieleman, D. van der Spoel and H.J.C. Berendsen
Molecular Dynamics Simulations of Dodecylphosphocholine Micelles at Three Different Aggregate Sizes: Micellar Structure and Chain Relaxation
J. Phys. Chem. B 104 (2000) 6380-6388

00.14
H.P. Lüthi
Metacomputing, an emerging technology?
Comput. Phys. Commun. 128 (2000) 326-332

00.15
A.M.J.J. Bonvin, A.E. Mark and W.F. van Gunsteren
The GROMOS96 Benchmarks for Molecular Simulation
Comput. Phys. Commun. 128 (2000) 550-557

00.16
C. Peter, X. Daura and W.F. van Gunsteren
Peptides of Aminoxy Acids: a Molecular Dynamics Simulation Study of Conformational Equilibria under Various Conditions
J. Am. Chem. Soc. 122 (2000) 7461-7466

00.17
S. Voordijk, T. Hansson, D. Hilvert and W.F. van Gunsteren
Molecular Dynamics Simulations Highlight Mobile Regions in Proteins: A Novel Suggestion for Converting a Murine VH Domain into a More Tractable Species
J. Mol. Biol. 300 (2000) 963-973

00.18
H. Schäfer
Calculation of Free Energy and Entropy from Molecular Simulations: Methodology and Application
Thesis, ETH Zürich, September 2000

00.19
R. Walser
Molecular Dynamisc Simulations: Solvent Properties and Solvent Effects on Proteins
Thesis, ETH Zürich, September 2000

00.20
R.R. Tykwinski, A. Hilger, F. Diederich, H.P. Lüthi, P. Seiler, V. Gramlich, J.-P. Gisselbrecht, C. Boudon and M. Gross
Donor-Acceptor-Functionalized Tetraethynylethenes with Nitrothienyl Substituents: Structure-Property Relationships
Helvetica Chim. Acta 83 (2000) 1484-1508

00.21
U. Stocker, K. Spiegel and W.F. van Gunsteren
On the similarity of properties in solution or crystalline state: A molecular dynamics study of hen lysozyme
J. Biomol. NMR 18 (2000) 1-12

00.22
L.D. Schuler and W.F. van Gunsteren
On the Choice of Dihedral Angle Potential Energy Functions for n-Alkanes
Mol. Simulation 25 (2000) 301-319

00.23
C.D. Berweger, W. Thiel and W.F. van Gunsteren
Molecular-Dynamics Simulation of the ß Domain of Methallothionein with a Semi-Empirical Treatment of the Metal Core
Proteins 41 (2000) 299-315

00.24
J.W. Pitera and P.A. Kollman
Exhaustive Mutagenesis In Silico: Multicoordinae Free Energy Calculations on Proteins and Peptides
Proteins 41 (2000) 385-397

00.25
H. Schäfer, A.E. Mark and W.F. van Gunsteren
Absolute entropies from molecular dynamics simulation trajectories
J. Chem. Phys. 113 (2000) 7809-7817

00.26
P.H. Hünenberger
Optimal charge-shaping functions for the particle-particle-particle-mesh (P3M) method for computing electrostatic interactions in molecular simulations
J. Chem. Phys. 113 (2000) 10464-10476

00.27
L. Schuler
Molecular Dynamics Simulation of Aggregates of Lipids: Development of Force-Field Parameters and Applications to Membranes and Micelles
Thesis, ETH Zürich, December 2000

00.28
B.C. Oostenbrink, J.W. Pitera, M.M.H. van Lipzig, J.H.N. Meerman and W.F. van Gunsteren
Simulations of the Estrogen Receptor Ligand Binding Domain: the affinity of natural ligands and xenoestrogens
J. Med. Chem. 43 (2000) 4594-4605

00.29
S. Portmann, A. Inauen, H.P. Lüthi and S. Leutwyler
Chiral discimination in hydrogen-bonded complexes
J. Chem. Phys. 113 (2000) 9577-9585

00.30
W. Alda, D.A. Yuen, H.P. Lüthi amd J. Rustad
Exothermic and Endothermic Chemical Reactions Involving Very Many Particles Modelled with Molecular Dynamics
Physica D 146 (2000) 261-

00.31
M.J. Mayor-Loopez, H.P. Lüthi, H. Koch, P.-Y. Morgantini and J. Weber
Coupled-cluster calculations on ferrocene and its protonated derivative: towards the final word on the mechanism of protonation of ferrocene?
J. Chem. Phys. 113 (2000) 8009-8014

00.32
S. Portmann and H.P. Lüthi
MOLEKEL: An Interactive Molecular Graphics Tool
Chimia 54 (2000) 766-770

00.33
S.J. Marrink, D.P. Tieleman and A.E. Mark
Molecular Dynamics Simulation of the Kinetics of Spontaneous Micelle Formation
J. Phys. Chem. B 104 (2000) 12165-12173

00.34
M. Fioroni, K. Burger, A.E. Mark and D. Roccatano
A New 2,2,2-Trifluoroethanol Model for Molecular Dynamics Simulations
J. Phys. Chem. B. 104 (2000) 12347-12354

2001

01.1
W.F. van Gunsteren, R. Bürgi, C. Peter and X. Daura
The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State
Angew. Chemie Intl. Ed. 40 (2001) 351-355

01.2
R. Walser and W.F. van Gunsteren
Viscosity Dependence of Protein Dynamics
Proteins 42 (2001) 414-421

01.3
F.A. Hamprecht
Modern Methods for the Analysis of Multi-dimensional Data in the Natural Sciences
Thesis, ETH Zürich, February 2001

01.4
F.A. Hamprecht, C. Peter, X. Daura, W. Thiel and W.F. van Gunsteren
A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering and visualization
J. Chem. Phys. 114 (2001) 2079-2089

01.5
R. Bürgi, X. Daura, A. Mark, M. Bellanda, S. Mammi, E. Peggion and W.F. van Gunsteren
Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations
J. Peptide Res. 57(2001) 107-118

01.6
M. Bellanda, E. Peggion, R. Bürgi, W.F. van Gunsteren and S. Mammi
Conformational study of an Aib-rich peptide in DMSO by NMR
J. Peptide Res. 57 (2001) 97 - 106

01.7
S.R. Billeter, C.F.W. Hanser, T.Z. Mordasini, M. Scholten, W. Thiel and W.F. van Gunsteren
Molecular dynamics study of oxygenation reactions catalysed by the enzyme p-hydroxybenzoate hydroxylase
Phys. Chem. Chem. Phys. 3 (2001) 688-695

01.8
V. Kräutler, W.F. van Gunsteren and P.H. Hünenberger
A Fast SHAKE Algorithm to Solve Distance Constraint Equations for Small Molecules in Molecular Dynamics Simulations
J. Comput. Chem. 22 (2001) 501-508

01.9
S. Tsuzuki and H.P. Lüthi
Interaction energies of van der Waals and hydrogen bonded systems calculated using density functional theory: Assessing the PW91 model
J. Chem. Phys. 114 (2001) 3949-3957

01.10
X. Daura, K. Gademann, H. Schäfer, B. Jaun, D. Seebach and W.F. van Gunsteren
The ß-Peptide Hairpin in Solution: Conformational Study of a ß-Hexapeptide in Methanol by NMR Spectroscopy and MD Simulation
JACS 123 (2001) 2393-2404

01.11
H. Schäfer, X. Daura, A.E. Mark and W.F. van Gunsteren
Entropy Calculations on a Reversibly Folding Peptide: Changes in Solute Free Energy Cannot Explain Folding Behaviour
Proteins 43 (2001) 45-56

01.12
J.W. Pitera and W.F. van Gunsteren
The Importance of Solute-Solvent van der Waals Interactions with Interior Atoms of Biopolymers
JACS 123 (2001) 3163-3164

01.13
R. Walser, B. Hess, A.E. Mark and W.F. van Gunsteren
Further investigation on the validity of Stokes-Einstein behaviour at the molecular level
Chem. Phys. Letters 334 (2001) 337-342

01.14
R. Bürgi, J. Pitera and W.F. van Gunsteren
Assessing the effect of conformational averaging on the measured values of observables
J. Biomol. NMR 19 (2001) 305-320

01.15
R.A. King, H.P. Lüthi, H.F. Schaefer III, F. Glarner and U. Burger
The Photohydration of N-Alkylpyridinium Salts: Theory and Experiment
Chem. Eur. J. 7 (2001) 1734-1742

01.16
R. Walser, P.H. Hünenberger and W.F. van Gunsteren
Comparison of Different Schemes to Treat Long-Range Electrostatic Interactions in Molecular Dynamics Simulations of a Protein Crystal
Proteins 43 (2001) 509-519

01.17
C.F. Wong, P.H. Hünenberger, P. Akamine, N. Nrayana, T. Diller, J.A. McCammon, S. Taylor and N.H. Xuong
Computational Analysis of PKA-Balanol Interactions
J. Med. Chem. 44 (2001) 1530-1539

01.18
U. Börjesson and P.H. Hünenberger
Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines
J. Chem. Phys. 114 (2001) 9706-9719

01.19
R. Zangi, H. Kovacs, W.F. van Gunsteren, J. Johansson and A.E. Mark
Free Energy Barrier Estimation of Unfolding the alpha-Helical Surfactant-Associated Polypeptide C
Proteins 43 (2001) 395-402

01.20
B.L. de Groot, X. Daura, A.E. Mark and H. Grubmüller
Essential dynamics of revesible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds
J. Mol. Biol. 309 (2001) 299-313

01.21
D.P. Tieleman, H.J.C. Berendsen and M.S.P. Sansom
Voltage-Dependent Insertion of Alamethicin at Phospholipid/Water and Octane/Water Interfaces
Biophys. J. 80 (2001) 331-346

01.22
R.P. Bürgi
Towards Understanding Polypeptide Structure and Titration: Theoretical Studies and Computer Simulations
thesis no 14244, ETH Zürich, June 2001

01.23
W.F. van Gunsteren, D. Bakowies, W. Damm, T. Hansson, U. Stocker and X. Daura
Practical Aspects of Simulation Studies of Biomolecular Systems
in: Dynamics, Structure and Function of Biological Macromolecules, O. Jardetzky and M.D. Finucane, eds., NATO ASI Series A315, IOS Press, Amsterdam, 2001, pp. 1-26

01.24
J.W. Pitera, M. Falta and W.F. van Gunsteren
Dielectric Properties of Proteins from Simulation: The effects of Solvent, Ligands, pH, and Temperature
Biophys. J. 80 (2001) 2546-2555

01.25
S.J. Marrink and A.E. Mark
Effect of Undulations on Surface Tension in Simulated Bilayers
J. Phys. Chem. B 105 (2001) 6122-6127

01.26
L.D. Schuler, X. Daura and W.F. van Gunsteren
An Improved GROMOS96 Force Field for Aliphatic Hydrocarbons in the Condensed Phase
J. Comput. Chem. 22 (2001) 1205-1218

01.27
U. Stocker and W.F. van Gunsteren
Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin
in: Crystallography of Biological Macromolecules, M.G. Rossmann amd E. Arnold, eds., Intl. Tables for Crystallography, Volume F, Kluwer Academic Publishers, Dordrecht, NL, 2001, pp. 481-495

01.28
T.N. Heinz, W.F. van Gunsteren and P.H. Hünenberger
Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations
J. Chem. Phys. 115 (2001) 1125-1136

01.29
L. Gobbi, N. Elmaci, H.P. Lüthi and F. Diederich
N,N-Dialkylaniline-Substituted Tetraethynylethenes: a New Class of Chromophores Possessing an Emitting Charge-Transfer State. Experimental and Computational Studies
Chem. Phys. Chem. 2 (2001) 432-433

01.30
W. Czechtizky, X. Daura, A. Vasella and W.F. van Gunsteren
Oligonucleotide Analogues with a Nucleobase-Including Backbone. Part 7: Molecular Dynamics Simulation of a DNA Duplex Containing a 2'-Deoxyadenosine 8-(Hydroxymethyl)-Derived Nucleotide
Helv. Chim. Acta 84 (2001) 2132-2145

01.31
C. Peter, X. Daura and W.F. van Gunsteren
Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations
J. Biomol. NMR 20 (2001) 297-310

01.32
L.D. Schuler, P. Walde, P.L. Luisi and W.F. van Gunsteren
Molecular dynamics simulation of n-dodecyl phosphate aggregate structures
Europ. Biophys. J. 30 (2001) 330-343

01.33
D. Roccatano, A.E. Mark and S Hayward
Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation
J. Mol. Biol. 310 (2001) 1039-1053

01.34
W.F. van Gunsteren, D. Bakowies, R. Bürgi, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, A. Glättli, T. Hansson, C. Oostenbrink, C. Peter, J. Pitera, L. Schuler, T. Soares and H. Yu
Molecular Dynamics Simulation of Biomolecular Systems
CHIMIA 55 (2001) 856-860

01.35
P.H. Hünenberger, U. Börjesson and R.D. Lins
Electrostatic Interactions in Biomolecular Systems
CHIMIA 55 (2001) 861-866

01.36
F.A. Hamprecht, D. Jost, M. Rüttimnn, F. Calamai and J.J. Kowalski
Preliminary results on the prediction of countershock succes with fibrillation power
Rescuscitation 50 (2001) 297-299

01.37
F.A. Hamprecht, U. Achleitner, A.C. Krismer, K.H. Lindner, V. Wenzel, H.-U. Strohmenger, W. Thiel and W.F. van Gunsteren
An alternative method of ECG spectral analysis for improved prediction of countershock success in a porcine model of ventricular fibrillation
Rescuscitation 50 (2001) 287-296

01.38
L.D. Creveld, W. Meijberg, H.J.C Berendsen and H.A.M. Pepermans
DSC studies of Fusarium solani pisi cutinase: consequences for stability in the presence of surfactants
Biophys. Chem. 92 (2001) 65-75

01.39
H.J.C. Berendsen
Slow Events in Complex Systems: Potential of Mean Force and the Smouchowski limit in biological systems
Simu Newsletter 3 (2001) 33-50

01.40
M. Fiorini, K. Burger, A.E. Mark and D. Roccatano
Model of 1,1,1,3,3,3-Hexafluoro-propan-2-ol for Molecular Dynamics Simulations
J. Phys. Chem. B 105 (2001) 10967-10975

01.41
R. Bürgi, F. Läng and W.F. van Gunsteren
A Comparison of Seven Fast but Approximate Methods to Compute the Free Energy of Deprotonation for Amino Acids in Aqueous Solution
Mol. Simulation 27 (2001) 215-236

01.42
J.W. Pitera and W.F. van Gunsteren
One-Step Perturbation Methods for Solvation Free Energies of Polar Solutes
J. Phys. Chem. B 105 (2001) 11264-11274

01.43
W.F. van Gunsteren, R. Bürgi, C. Peter and X. Daura
Reply to the Comment on the Communication by van Gunsteren et al., Angew. Chem. Int. Ed. 40 (2001) 351-355
Angew. Chem. Int. Ed. 40 (2001) 4617-4618

01.44
I. Chandrasekhar and W.F. van Gunsteren
Sensitivity of Molecular Dynamics Simulations of Lipids to the Size of the Ester Carbon
Current Science 81 (2001) 1325-1327

2002

02.1
B. Hess
Stochastic Concepts in Molecular Simulation
thesis, Univ. of Groningen, The Netherlands, January 2002

02.2
H. Schäfer, L.J. Smith, A.E. Mark and W.F. van Gunsteren
Entropy Calculations of the Molten Globule State of a Protein: Side-Chain Entropies of alpha-Lactalbumin
Proteins 46 (2002) 215-224

02.3
J.W. Pitera and W.F. van Gunsteren
A Comparison of Non-bonded Scaling Approaches for Free Energy Calculations
Mol. Simulation 28 (2002) 45-65

02.4
G. Colombo, D. Roccatano and A.E. Mark
Folding and Stability of the Three-Stranded beta-Sheet Peptide Betanova: Insights from Molecular Dynamics Simulations
Proteins 46 (2002) 380-392

02.5
A. Villa and A.E. Mark
Calculation of the Free Energy of Solvation for Neutral Analogues of Amino Acid Side Chains
J. Comput. Chem. 23 (2002) 548-553

02.6
P.J. Gee, F.A. Hamprecht, L.D. Schuler, W.F. van Gunsteren, E. Duchardt, H. Schwalbe, M. Albert and D. Seebach
A Molecular-Dynamics Simulation Study of the Conformational Preferences of Oligo-(3-hydroxy-alkanoic acids) in Chloroform Solution
Helv. Chim. Acta 85 (2002) 618-632

02.7
F.A. Hamprecht, W. Thiel, W.F. van Gunsteren
Chemical Library Subset Selection Algorithms: A Unified derivation Using Spatial Statistics
J. Chem. Inf. Comput. Sci. 42 (2002) 414-428

02.8
T. Hansson, C. Oostenbrink and W.F. van Gunsteren
Molecular Dynamics Simulations
Curr. Opinion Struct. Biol. 12 (2002) 190-196

02.9
C. Peter, W.F. van Gunsteren and P.H. Hünenberger
Solving the Poisson equation for solute-solvent systems using fast Fourier transforms
J. Chem. Phys. 116 (2002) 7434-7451

02.10
P.H. Hünenberger
Calculation of the group-based pressure in molecular simulations: I. A general formulation including Ewald and particle-particle-particle-mesh electrostatics
J. Chem. Phys. 116 (2002) 6880-6897

02.11
B. Oliva and P.H. Hünenberger
Calculation of the group-based pressure in molecular simulations: II. Numerical tests and application to liquid water
J. Chem. Phys. 116 (2002) 6898-6909

02.12
I. Chandrasekhar and W.F. van Gunsteren
A Comparison of the Potential Energy Parameters of Aliphatic Alkanes.
Molecular Dynamics Simulations of Triacylglycerols in the Alpha Phase.
Europ. Biophys. J. 31 (2002) 89-101

02.13
D. Bakowies and W.F. van Gunsteren
Simulations of apo- and holo- Fatty Acid Binding Protein: Structure and Dynamics of Protein, Ligand and Internal Water
J. Mol. Biol. 315 (2002) 713-736

02.14
C. Jamorski, J.B. Foresman, C. Thilgen and H.P. Lüthi
Assessment of time-dependent density-functional theory for the calculation of critical features in the absorption spectra of a series of aromatic donor-acceptor systems.
J. Chem. Phys. 116 (2002) 8761-8771

02.16
S.J. Marrink and A.E. Mark
Molecular Dynamics Simulations of Mixed Micelles Modeling Human Bile
Biochemistry 41 (2002) 5375-5382

02.17
M.G. Pikkemaat, A.B.M. Linssen, H.J.C. Berendsen and D.B. Janssen
Molecular dynamics simulations as a tool for improving protein stability
Protein Engineering 15 (2002) 185-192

02.18
A. Glättli, X. Daura and W.F. van Gunsteren
Derivation of an improved SPC model for liquid water: SPC/A and SPC/L
J. Chem. Phys. 116 (2002) 9811-9828

02.19
D. Bakowies and W.F. van Gunsteren
Water in Protein Binding Cavities: Implementation of a Method to Identify Internal Water and Exchange Pathways and Application to Fatty Acid Binding Protein
Proteins 47 (2002) 534-545

02.20
R. Bürgi, P.A. Kollman and W.F. van Gunsteren
Simulating Proteins at Constant pH: An Approach Combining Molecular Dynamics and Monte Carlo Simulation
Proteins 47 (2002) 469-480

02.21
G. Groenhof, M.F. Lensink, H.J.C. Berendsen, J.G. Snijders and A.E. Mark
Signal Transduction in the Photoactive Yellow Protein. I: Photon Absorption and the Isomerization of the Chromophore
Proteins 48 (2002) 202-211

02.22
G. Groenhof, M.F. Lensink, H.J.C. Berendsen and A.E. Mark
Signal Transduction in the Photoactive Yellow Protein. II: Proton Transfer Initiates Conformational Changes
Proteins 48 (2002) 212-219

02.23
R. Zangi, M.L. de Vocht, G.T. Robillard and A.E. Mark
Molecular Dynamics Study of the Folding of Hydrophobin SC3 at a Hydrophilic/Hydrophobic Interface
Biophys. J. 83 (2002) 112-124

02.24
J.A. Flohil, G. Vriend and H.J.C Berendsen
Completion and Refinement of 3-D Homology Models with Restricted Molecular Dynamics: Application to Targets 47, 58, and 111 in the CASP Moedeling Competition and Posterior Analysis
Proteins 48 (2002) 593-604

02.25
L.J. Smith, X. Daura and W.F. van Gunsteren
Assessing equilibration and convergence in biomolecular simulations
Proteins 48 (2002) 487-496

02.26
F. van Lune, L. Manning. K. Dijkstra, H.J.C. Berendsen and R.M. Scheek
Order-parameter tensor description of HPr in a medium of oriented bicelles
J. Biomol. NMR 23(2002) 169-179

02.27
A.N. Morozov
Orientational Transitions in Bock-Copolymer Melts under Shear Flow
thesis, Univ. of Groningen, The Netherlands, February 2002

02.28
K.A. Feenstra
Long Term Dynamics of Proteins and Peptides
thesis, Univ. of Groningen, The Netherlands, July 2002

02.29
B. Hess, H. Saint-Martin and H.J.C. Berendsen
Flexible constraints: An adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable MCDHO model for water
J. Chem. Phys. 116(2002) 9602-9610

02.30
R. Walser, P.H. Hünenberger and W.F. van Gunsteren
Molecular Dynamics Simulations of a Double Unit Cell in a Protein Crystal: Volume Relaxation at Constant Pressure and Correlation of Motion between the Two Unit Cells
Proteins 48 (2002) 327-340

02.31
K.A. Feenstra, C. Peter, R.M. Scheek, W.F.van Gunsteren and A.E. Mark
A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities in small peptides
J. Biomol. NMR 23 (2002) 181-194

02.32
C. Jamorski Jödicke and H.P. Lüthi
Time-dependent density-functional theory investigation of the formation of the charge transfer exited state
for a series of aromatic donor-acceptor systems. Part I
J. Chem. Phys. 117 (2002) 4146-4156

02.33
W.F. van Gunsteren
Computersimulatie van complexe (bio)moleculaire systemen: Mogelijkheden, onmogelijkheden en perspectieven
NWO/Huygens-lezing, Den Haag, NL, 14.11.2001, NWO, Den Haag, 2002
(only available in Dutch)

02.34
M.F. Lensink
Non-adiabatic Proton Transfer in Biomolecular Systems
thesis, Univ. of Groningen, The Netherlands, March 2002

02.35
E. AB
Structural Studies on IIBChb
thesis, Univ. of Groningen, The Netherlands, June 2002

02.36
P.A.W. van den Berg, K.A. Feenstra, A.E. Mark, H.J.C. Berendsen and A.J.W.G. Visser
Dynamic Conformations of Flavin Adenine Dinucleotide: Simulated Molecular Dynamics of the Flavin Cofactor Related to the Time-Resolved Fluorescence Characteristics
J. Phys. Chem. B 106 (2002) 8858-8869

02.37
C. Jamorski Jödicke and H.P. Lüthi
Time-dependent density-functional theory investigation of the formation of the charge transfer excited state for a series of aromatic donor-acceptor systems - Part II
J. Chem. Phys. 117 (2002) 4157-4167

02.38
W.F. van Gunsteren, X. Daura and A.E. Mark
Computation of Free Energy
Helv. Chim. Acta 85 (2002) 3113-3129

02.39
D. Kony, W. Damm, S. Stoll and W.F. van Gunsteren
An Improved OPLS-AA Force Field for Carbohydrates
J. Comput. Chem. 23 (2002) 1416-1429

02.40
A. Glättli, X. Daura, D. Seebach and W.F. van Gunsteren
Can one derive the conformational preference of a beta-peptide from its CD spectrum?
J. Am. Chem. Soc. 124 (2002) 12972-12978

02.41
D. Roccatano, G. Colombo, M. Fioroni and A.E. Mark
Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary structure formation in peptides: A molecular dynamics study
Proc. Natl. Acad. Sci. 99 (2002) 12179-12184

02.42
X. Daura, A. Glättli, P. Gee, C. Peter and W.F. van Gunsteren
The Unfolded State of Peptides
Adv. Prot. Chem. 62 (2002) 341-360

02.43
R. Baron, D. Bakowies, W.F. van Gunsteren and X. Daura
Beta-Peptides with Different Secondary-Structure Preferences: How Different Are Their Conformational Spaces?
Helv. Chim. Acta 85 (2002) 3872-3882

02.44
I. Antes, W. Thiel and W.F. van Gunsteren
Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation
Europ. Biophys. J. 31 (2002) 504-520

02.45
P. Soto and A.E. Mark
The effect of the neglect of electronic polarization in peptide folding simulations
J. Phys. Chem. B 106 (2002) 12830-12833

02.46
D. Seebach, T. Sifferlen, D. Bierbaum, M. Rueping, B. Jaun, B. Schweizer, J. Schaefer, A.K. Mehta, R.D. O'Connor, B.H. Meier, M. Ernst and A. Glättli
Isotopically Labelled and Unlabelled ß-Peptides with Geminal Dimethyl-Substitution in 2-Position of Each Residue - Synthesis and NMR-Investigation in Solution and in the Solid State
Helv. Chim. Acta 85 (2002) 2877-2917

02.47
S.S. Park, K.H. Lee, Y. Suh, C. Lee and H.P. Lüthi
Geometries and Relative Stabilities of AIN Four-Membered-Ring Compound Isomers: Ab initio Study
Bull. Korean Chem. Soc. 23 (2002) 241-244

02.48
M.E.F. Apol, H.J.C. Berendsen, A.E. Mark and A.C. Hoffmann
Interparticle Forces for DEM by MD Simulations
Proceed. 4th World Congr. on Particle Tech., Sydney (2002)

2003

03.1
U. Stocker, D. Juchli and W.F. van Gunsteren
Increasing the time step and efficiency of molecular dynamics simulations: optimal solutions for equilibrium simulations or structure refinement of large biomolecules
Mol. Simulation 29 (2003) 123-138

03.2
H. Yu, T Hansson and W.F. van Gunsteren
Development of a Simple, Self-Consistent Polarizable Model for Liquid Water
J. Chem. Phys. 118 (2003) 221-234

03.3
C. Jamorski Jödicke and H.P. Lüthi
Time-depedent density-functional theory (TDDFT) study of the excited charge transfer state formation of a series of aromatic donor-acceptor systems
J. Am. Chem. Soc. 125 (2003) 252-264

03.4
I. Chandrasekhar, M. Kastenholz, R.D. lins, C. Oostenbrink, L.D. Schuler, D.P. Tieleman and W.F. van Gunsteren
A consistent potential energy parameter set for lipids: Dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field
Europ. Biophys. J. 32 (2003) 67-77

03.5
C. Jamorski Jödicke and H.P. Lüthi
A time-dependent density-functional theory investigation of the fluorescence behavior of related cyano and dicyano isomers of 4-(N,N-dimethylamino)benzonitrile
Chem. Phys. Let. 368 (2003) 561-567

03.6
G. Colombo, S.J. Marrink and A.E. Mark
Simulation of MscL Gating in a Bilayer under Stress
Biophys. J. 84 (2003) 2331-2337

03.7
C. Peter
A Critical Analysis of Various Aspects of Biomolecular Simulation: from Electrostatic Forces, NMR Spectra, and Entropy to Peptide Folding
thesis no 15160, ETH Zürich, June 2003

03.8
A. Glättli, X. Daura and W.F. van Gunsteren
A Novel Approach for Designing Simple Point Charge Models for Liquid Water with Three Interaction Sites
J. Comput. Chem. 24 (2003) 1087-1096

03.9
D. Bakowies
Trendberichte Theoretische Chemie 2003: Kraftfelder für biomolekulare Simulationen
Nachr. Chem. 51 (2003) 325-327

03.10
D. Bakowies
Trendberichte Theoretische Chemie 2003: Biomolekulare Reality-Simulationen
Nachr. Chem. 51 (2003) 788-793

03.11
R. Zangi and A.E. Mark
Monolayer Ice
Physical Review Letters 91 (2003)

03.12
R. Zangi and A.E. Mark
Bilayer ice and alternate liquid phases of confined water
J. Chem. Phys. 119 (2003) 1694-1700

03.13
M. Fioroni, K. Burger, A.E. Mark and D. Roccatano
The Influence of Trifluoromethyl Groups on the Miscibility of Fluorinated Alcohols with Water: A Molecular Dynamics Simulation Study of 1,1,1-Trifluoropropan-2-ol in Aqueous Solution
J. Phys. Chem. B 107 (2003) 4855-4861

03.14
D.P. Tieleman, H. Leontiadou, A.E. Mark and S.-J. Marrink
Simulation of Pore Formation in Lipid Bilayers by Mechanical Stress and Electric Fields
JACS 125 (2003) 6382-6283

03.15
M. Bergdorf, C. Peter and P.H. Hünenberger
Influence of cutoff truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: a continuum electrostatics study
J. Chem. Phys. 119 (2003) 9129-9144

03.16
R. Gargallo, P.H. Hünenberger, F.X. Avilés and B. Oliva
Molecular Dynamics simulation of highly-charged proteins: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions
Prot. Sci. 12 (2003) 2161-2172

03.17
C. Oostenbrink and W.F. van Gunsteren
Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility and character
J. Comput. Chem. 24 (2003) 1730-1739

03.18
U. Börjesson and P.H. Hünenberger
Effect of mutations involving charged residues on the stability of Staphylococcal nuclease: A continuum electrostatics study
Protein Engineering 16 (2003) 831-840

03.19
C. Peter, W.F. van Gunsteren and P.H. Hünenberger
A fast-Fourier-transform method to solve continuum-electrostatics problems with truncated electrostatic interactions: algorithm and application to ionic solvation and ion-ion interaction
J. Chem. Phys. 119 (2003) 12205-12223

03.20
X. Daura, D. Bakowies, D. Seebach, J. Fleischhauer, W.F. van Gunsteren and P. Krüger
Circular dichroism spectra of Â-peptides: Sensitivity to molecular structure and effects of motional averaging
Eur. Biophys. J. 32 (2003) 661-670

03.21
C. Peter, M. Rüping, H.J. Wörner, B. Jaun, D. Seebach and W.F. van Gunsteren
Molecular dynamics simulations of small peptides: Can one derive conformational preferences from ROESY spectra ?
Chem. Eur. J. 9 (2003) 5838-5849

03.22
K.H. Lee, C.Lee, S.S. Park, Y. Kim, H.P. Lüthi, S.Lee, Y.S. Lee
Structures and energetics of borafullerene dimmer conformers
Synthetic Met 125 (2003) 723

03.23
R. Talhout, A. Villa, A.E. Mark and J.B.F.N. Engeberts
Understanding Binding Affinity: A Combined Isothermal Tritration Calorimetry/Molecular Dynamics Study of the Binding of a Series of Hydrophobically Modified Benzamidinium Chloride Inhibitors to Trypsin
J. Am. Chem. Soc. 125 (2003) 10570-10579

03.24
C. Jamorski Jödicke and H.P. Lüthi
Rational classification of a series of aromatic donor-acceptor systems within the TICT model, a time-dependent density-functional theory investigation
J. Chem. Phys. 119 (2003) 12852 - 12865

03.25
H. Fan and A.E. Mark
Relative Stability of Protein Structures Determined by X=ray Crystallography or NMR Spectroscopy: A Molecular Dynamics Simulation Study
Proteins 53 (2003) 111 - 120

03.26
S.J. Marrink and A.E. Mark
Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles
J. Am. Chem. Soc. 125 (2003) 15233 - 15242

03.27
S.J. Marrink and A.E. Mark
The Mechanism of Vesicle Fusion as Revealed by Molecular Dynamics Simulations
J. Am. Chem. Soc. 125 (2003) 11144 - 11145

03.28
A. Villa, R. Zangi, G. Pieffet and A.E. Mark
Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to Factor Xa and Trypsin
J. Comp. Aided. Mol. Design 17 (2003) 673 - 686

2004

04.1
H. Yu, X. Daura and W.F. van Gunsteren
Molecular Dynamics Simulations of Peptides Containing an Unnatural Amino Acid: Dimerization, Folding and Protein Binding
Proteins 54 (2004) 116-127

04.2
M.A. Kastenholz and P.H. Hünenberger
Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum-methods
J. Phys. Chem. B 108 (2004) 774-778

04.3
C. Oostenbrink and W.F. van Gunsteren
Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation
Proteins 54 (2004) 234-246

04.4
N.F.A. van der Vegt and W.F. van Gunsteren
Entropic Contributions in co-Solvent Binding to Hydrophobic Solutes in Water
J. Phys. Chem. B 108 (2004) 1056-1064

04.5
L.J. Smith, H.J.C. Berendsen and W.F. van Gunsteren
Computer Simulation of Urea-Water Mixtures: A Test of Force Field Parameters for Use in Biomolecular Simulations
J. Phys. Chem. B 108 (2004) 1065-1071

04.6
D.P. Geerke, C. Oostenbrink, N.F.A. van der Vegt and W.F. van Gunsteren
An Effective Force Field for Molecular Dynamics Simulations of Dimethyl Sulfoxide and Dimethyl Sulfoxide-Water Mixtures
J. Phys. Chem. B 108 (2004) 1436 - 1445

04.7
D. Trzesniak, N.F.A. van der Vegt, W.F. van Gunsteren
Computer simulation studies on the solvation of aliphatic hydrocarbons in 6.9 M aqueous urea solution
Phys. Chem. Chem. Phys. 6 (2004) 697-702

04.8
N.F.A. van der Vegt, D. Trzesniak, B. Kasumaj and W.F. van Gunsteren
Energy-Entropy Compensation in the Transfer of Nonpolar Solutes from Water to Co-Solvent/Water Mixtures
Chem. Phys. Chem. 5 (2004) 144-147

04.9
C. Peter, C. Oostenbrink, A. van Dorp, W.F. van Gunsteren
Estimating entropies from molecular dynamics simulations
J. Chem. Phys. 120 (2004) 2652-2661

04.10
A. Glättli, C. Oostenbrink, X. Daura, D.P. Geerke, H. Yu, W.F. van Gunsteren
On the transferability of the SPC/L water model to biomolecular simulation
Brazilian J. of Phys. 34 (2004) 116-125

04.11
A.H. de Vries, A.E. Mark and S.-J. Marrink
The Binary Mixing Behaviour of Phospholipids in a Bilayer: a Molecular Dynamics Study
J. Phys. Chem. B 108 (2004) 2454-2463

04.12
H. Fan and A.E. Mark
Refinement of homology-based protein structures by molecular dynamics simulation techniques
Protein Science 13 (2004) 211-220

04.13
H. Leontiadou, A.E. Mark and S.J. Marrink
Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers
Biophysical Journal 86 (2004) 2156 - 2164

04.14
U. Börjesson
Electrostatic interactions in computer simulations of biomolecular systems: influence of system size, solvation and titration
thesis no. 15454, ETH Zürich, February 2004

04.15
R.D. Lins, C.S. Pereira and P.H. Hünenberger
Trehalose-Protein Interaction in Aqueous Solution
Proteins 55 (2004) 177 - 186

04.16
C.S. Pereira, R.D. Lins, I. Chandrasekhar, L.C.G. Freitas, P.H. Hünenberger
Interaction of the Disaccharide Trehalose with a Phospholipid Bilayer: A Molecular Dynamics Study
Biophysical Journal 86 (2004) 2273 - 2285

04.17
S. Calero, S. Lago, W.F. van Gunsteren, X. Daura
Modelling of the complex between a 15-residue peptide from mSos2 and the N-terminal SH3 domain of Grb2 by molecular dynamics simulation
Chem. Biodiv. 1 (2004) 505 - 519

04.18
A.H. de Vries, A.E. Mark, S.J. Marrink
Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle n water in atomistic detail
J. Am. Chem. Soc. 126 (2004) 4488 - 4489

04.19
H. Fan and A.E. Mark
Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures
Protein Science 13 (2004) 992 - 999

04.20
R. Zangi and A.E. Mark
Electrofreezing of confined water
J. Chem. Phys. 120 (2004) 7123 - 7130

04.21
G. Groenhof, M. Bouxin-Cademartory, B. Hess, S.P. de Visser, H.J.C. Berendsen, M Olivucci, A.E. Mark, M.A. Robb
Photoactivation of the Photoactive Yellow Protein: Why photo absorption triggers a trans-to-cis isomerization of the chromophore in the Protein
J. Am. Chem. Soc. 126 (2004) 4228 - 4233

04.22
S.J. Marrink, A.H. de Vries and A.E. Mark
Coarse Grained model for Semiquantitative Lipid Simulations
J. Phys. Chem. B. 108 (2004) 750 - 760

04.23
D. Kony, W. Damm, S. Stoll and P.H. Hünenberger
Explicit-solvent molecular-dynamics simulations of the of (1-3)- and (1-6)-linked disaccharides -laminarabiose and -gentiobiose in water
J. Phys. Chem. B. 108 (2004) 5815 - 5826

04.24
T. Heinz and P.H. Hünenberger
A fast pairlist construction algorithm for molecular simulations under periodic boundary conditions
J. Comput. Chem. 25 (2004) 1474 - 1486

04.25
H. Yu, M. Amann, T. Hansson, J. Köhler, G. Wich, W.F. van Gunsteren
Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: A molecular dynamics study
Carbohydrate Research 339 (2004) 1697 - 1709

04.26
H. Yu, M. Ramseier, R. Bürgi, W.F. van Gunsteren
Comparison of properties of Aib-rich peptides in crystal and solution: A molecular dynamics study
Chem. Phys. Chem. 5 (2004) 633 - 641

04.27
I. Chandrasekhar, C. Oostenbrink and W.F. van Gunsteren
Simulating the Physiological Phase of Hydrated Dipalmitoylphosphatidylcholine Bilayers: The Ester Moiety
Soft Materials 2 (2004) 27 - 45

04.28
C. Oostenbrink, A. Villa, A.E. Mark and W.F. van Gunsteren
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6
J. Comp. Chem. (2004) 25 (2004) 1656 - 1676

04.29
A. Glättli
Computer simulation of biomolecular systems: From the formulation of models for water, to the interpretation of experiment, to the investigation of polypeptide folding and membrane protein dynamics
thesis no 15609, ETH Zürich, June 2004

04.30
R. Baron, D. Bakowies and W.F. van Gunsteren
Carbopeptoid folding: effects of stereochemistry, chain length and solvent
Angew. Chem. Int. Ed. Engl. 43 (2004) 4055-4059
Angew. Chem. 116 (2004) 4147-4151

04.31
H. Yu
Biomolecular simulation: inclusion of polarizability, prediction of conformational stability, and analysis of peptide folding and association
thesis no 15670, ETH Zürich, August 2004

04.32
T. Soares, M. Christen, K. Hu and W.F. van Gunsteren
α- and β-polypeptides show a different stability of helical secondary structure
Tetrahedron 60 (2004) 7775-7780

04.33
U. Börjesson and P.H. Hünenberger
pH-Dependent stability of a Decalysine α-Helix Studied by Explicit-Solvent Molecular Dynamics Simulations at Constant pH
J. Phys. Chem. B 108 (2004) 13551-13559

04.34
C.M. Santiveri, M.A. Jiménez, M. Rico, W.F. van Gunsteren and X. Daura
ß-Hairpin folding and stability: Molecular dynamics simulations of designed peptides in aqueous solution
J. Peptide Sci. 10 (2004) 546-565

04.35
A. Glättli and W.F. van Gunsteren
Are NMR-derived model structures for peptides representative for the ensemble of structures adopted in solution? Probing the fourth helical secondary structure of β-peptides by molecular dynamics simulation
Angew. Chem. Int. Ed. Engl. 43 (2004) 6312-6316
Angew. Chem. 116 (2004) 6472-6476

04.36
A. Glättli, D. Seebach and W.F. van Gunsteren
Do valine side-chains have an influence on the folding behavior of β-substituted β-peptides?
Helv. Chem. Act. 87 (2004) 2487-2506

04.37
M.G. Giuffreda, M. Bruschi and H.P. Lüthi
Electron Delocalization in Linearly π-Conjugated Systems: A Concept for Quantitative Analysis
Chem. Eur.J. 10 (2004) 5671-5680

04.38
M. van den Bosch, M. Swart, W.F. van Gunsteren and G.W. Canters
Simulation of the Substrate Cavity Dynamics of Quercetinase
J. Mol. Biol. 344 (2004) 725-738

04.39
S.J. Marrink and A.E. Mark
Molecular view of hexagonal phase formation in phospholipid membranes.
Biophys. J. 87 (2004) 3894-3900

04.40
H. Yu and W.F. van Gunsteren
Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice
J. Chem. Phys. 121 (2004) 9549-9564

04.41
R. Faller and S.J. Marrink
Simulation of daomain formation in DLPC-DSPC mixed bilayers
Langmuir 20 (2004) 7686-7693

04.42
T.A. Soares, X. Daura, C. Oostenbrink, L.J. Smith, W.F. van Gunsteren
Validation of the GROMOS Force-field Parameter Set 45A3 against Nuclear Magnetic Resonance Data of Hen Egg Lysozyme
J. Biomol. NMR 30 (2004) 407-422

04.43
C. Oostenbrink
Free energies from biomolecular simulation: Force fields, methodology and applications
thesis no 15748, ETH Zürich, October 2004

04.44
R. Zangi
Water confined to a slab geometry: a review of recent computer simulations studies
J. of Physics 16 (2004) 5371-5388

2005

05.01
C. Oostenbrink and W.F. van Gunsteren
Methane clustering in explicit water: Effect of urea on hydrophobic interactions
Phys.Chem.Chem.Phys. 7 (2005) 53-58

05.02
K. Pervushin, B. Vögeli, T.N. Heinz, P.H. Hünenberger
Measuring 1H-1H and 1H-13C RDCs in methyl groups: example of pulse sequences with numerically optimized coherence transfer schemes
J. Magn. Res. 172 (2005) 36-47

05.03
L.J. Smith, R.M. Jones and W.F. van Gunsteren
Characterisation of the denaturation of human α-lactalbumin in urea by molecular dynamics simulations
Proteins 58 (2005) 439-449

05.04
J. Dolenc, C. Oostenbrink, J. Koller and W.F. van Gunsteren
Molecular Dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site
Nucleic Acids Research 33 (2005) 725-733

05.05
R. Baron, D. Bakowies and W.F. van Gunsteren
Principles of Carbopeptoid Folding: A Molecular Dynamics Simulation Study
J. Peptide Science 11 (2005) 74-84

05.06
P.H. Hünenberger
Thermostat Algorithms for Molecular-Dynamics Simulations
Adv. Polym. Sci. 173 (2005) 105-149

05.07
T.A. Soares, P.H. Hünenberger, M.A. Kastenholz, V. Kräutler, T. Lenz, R.D. Lins, C. Oostenbrink and W.F. van Gunsteren
An Improved Nucleic-Acid Parameter Set for the GROMOS Force Field
J.Comp.Chem. 26 (2005) 725-737

05.08
M. van den Bosch, M. Swart, J.G. Snijders, H.J.C. Berensen, A.E. Mark, C. Oostenbrink, W.F.van Gunsteren and G.W.Canters
Calculation of the redox potential of the protein azurin and some mutants
ChemBioChem 6 (2005) 738-746

05.09
D. Kovalskyy, V. Dubyna, D. Kanibolotsky, A.E. Mark and A. Kornelyuk
A molecular dynamics study of the structural stability of HIB-1 protease under physiological conditions: The role of Na-ions in stabilizing the active site
Proteins 58 (2005) 450-458

05.10
P. Soto, J. Cladera, A.E. Mark and X. Daura
Stability of SIV gp32 Fusion Peptide Single Layer Protofibrils as Monitored by Molecular Dynamics Simulations
Angew.Chem 117 (2005) 1089-1091

05.11
S. Donnini, A.E. Mark, A.H. Juffer and A. Villa
Incorporating the effect of ionic strength in the free energy calculations using explicit ions
J.Comp.Chem. 26 (2005) 115-122

05.12
V. Knecht, M. Mueller, M. Bonn, S.J. Marrink and A.E. Mark
Simulation studies of pore and domain formation in a phospholipid monolayer
J.Chem.Phys. 122 (2005) 24704-24713

05.13
R. Zangi and J.B.F.N. Engberts
Physisorption of Hydroxide Ions from Aqueous Solution to a Hydrophobic Surface
JACS 127 (2005) 2272-2276

05.14
K. Pagel, K. Seeger, B. Weiwert, A. Villa, A.E. Mark, S. Berger and B. Koksch
Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide
Organic & Biomolecular Chemistry, 3 (2005) 1189-1194

05.15
C. Oostenbrink and W.F. van Gunsteren
Free energies of ligand binding for structurally diverse compounds
PNAS 102 (2005) 6750-6754

05.16
C. Oostenbrink, T.A. Soares, Nico F.A. van der Vegt and W.F. van Gunsteren
Validation of the 53A6 GROMOS force field
Eur. Biophys J. 34 (2005) 273-284

05.17
A.H. de Vries, I. Chandrasekhar, W.F. van Gunsteren and P.H. Hünenberger
Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system, size and simulation time
J. Phys. Chem. 109 (2005) 11643-11652

05.18
Y. Zhou, C. Oostenbrink, W.F. van Gunsteren, W.R. Hagen, S.R. de Leeuw and J.A. Jongejan
The relative Stability of Homochiral and Heterochiral Alanine Dipeptides. Effects of Perturbation Pahtways and Force-Field Parameters on Free Energy Calculations
Molecular Physics 103 (2005) 1961-1969

05.19
H. Fan, A.E. Mark, J. Zhu, B. Honig
Comparative study of generalized Born models; Protein dynamics
PNAS 102 (2005) 6760-6764

05.20
P. Gee
Studies relating to the numerical simulation of molecular dynamics
Thesis Nr. 15938, ETH Zuerich. 2005

05.21
S.D. Hsu, C. Peter, W.F. van Gunsteren and A.M.J.J. Bonvin
Entropy calculation of HIV-1 Env gp 120, its receptor CD4 and their complex: an analysis of entropy changes upon complexation
Biophys. J. 88 (2005) 15-24

05.22
C. Oostenbrink and W.F. van Gunsteren
Efficient calculation of stacking and pairing free energies in DNA from molecular dynamics simulations
Chem. Eur. J. 11 (2005) 4340-4348

05.23
B. Zagrovic, J. Lipfert, E.J. Sorin, I.S. Millett, W.F. van Gunsteren, S. Doniach and V.S. Pande
Unusual compactness of a polyproline type II structure
PNAS 102 (2005) 11698-11703

05.24
A. Aemisseger, V. Kräutler, W.F. van Gunsteren and D. Hilvert
A Photoinducible β-hairpin
JACS 127 (2005) 2929-2936

05.25
V. Kräutler, A. Aemisseger, P.H. Hünenberger, D. Hilvert, T. Hansson and W.F. van Gunsteren
Use of Molecular Dynamics in the Design and Structure Determination of a Photoinducible β-hairpin
JACS 127 (2005) 4935-4942

05.26
I. Chandrasekhar, D. Bakowies, A. Glättli, P.H. Hünenberger, C. Pereira and W.F. van Gunsteren
Molecular Dynamics Simulation of Lipid Bilayers with GROMOS96: Application of Surface Tension
Mol. Simulation 31 (2005) 543-548

05.27
R.D. Lins and P.H. Hünenberger
A new GROMOS force field for hexopyranose-based cardohydrates
J. Compt. Chem. 26 (2005) 1400-1412

05.28
J.H. Missimer, M.O. Steinmetz, W. Jahnke, F.K. Winkler, W.F. van Gunsteren and X. Daura
Molecular dynamics simulations of helical 16-residue C- and N-terminal peptide derivatives of GCN4-p1 in aqueous solution
Chem. & Biodiversity 2 (2005) 1086-1104

05.29
C. Oostenbrink, D. Juchli, W.F. van Gunsteren
Amine hydration: A united-atom force field solution
ChemPhysChem 6 (2005) 1800-1804

05.30
Bojan Zagrovic, Guha Jayachandran, Ian S. Millett, Sebastian Doniach and Vijay S. Pande
How large is α-helix in solution? Studies ot the radii of gyration of helical peptides by SAXS and MD
J. Mol. Biol. 353 (2005) 232-241

05.31
H. Yu and W.F. van Gunsteren
Accounting for polarization in molecular simulation
Comput.Phys.Commun. 172 (2005) 69-85

05.32
M. Christen, P.H. Hünenberger, D. Bakowies, R. Baron, R. Bürgi, D.P. Geerke, T.N. Heinz, M.A. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak, W.F. van Gunsteren
The GROMOS software for biomolecular simulation: GROMOS05
J. Comput. Chem. 26(2005) 1719-1751

05.33
A. Glättli, X. Daura, P. Bindschädler, B. Jaun, Y.R. Mahajan, R.I. Mathad, M.Rueping, D. Seebach an d W.F. van Gunsteren
On the influence of charged side-chains on the folding-unfolding equilibrium of β-peptides - A molecular dynamics simulation study
Chem. Eur. J. 11(2005) 7276-7293 and suppl. mat

05.34
A. Glättli, I. Chandrasekhar and W.F. van Gunsteren
Molecular dynamics study of the bee venom melittin in aqueous solution, in methanol, and inserted in a phospholipid bilayer
Eur. Biophys. J. (2005) on-line

05.35
M. Christen and W.F. van Gunsteren
An approximate but fast method to impose flexible distance constraints in molecular dynamics simulations
J. Chem. Phys. 122 (2005) 144106

05.36
T.N. Heinz and P.H. Hünenberger
Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations
J. Chem. Phys. 123 (2005) on-line

05.37
C. Oostenbrink and W.F. van Gunsteren
Calculating zeros: non-equilibrium free energy calculations
Chem. Phys. 323 (2006) 102-108

05.38
M. Bruschi, M.G. Giuffreda, H.P. Lüthi
Measuring Electron Delocalization in π-Conjugated Systems
CHIMIA 59 (2005) 539-544

05.39
M. Bruschi, M.G. Giuffreda, H.P. Lüthi
Through versus cross electron delocalization in polytriacetylene oligomers: A computational analysis
ChemPhysChem 6 (2005) 511-519

05.40
M.A. Kastenholz
Electrostatic interactions in computer simulations of (bio-)molecular system
Thesis Nr. 16342, ETH Zürich. 2005

05.41
M. Bruschi
Electron Delocalization in Linearly π-Conjugated Compounds; a New Approach of Analysis
Thesis Nr. 16343, ETH Zürich. 2005

05.42
D. Trzesniak, A. Glättli, B. Jaun and W.F. van Gunsteren
Interpreting NMR Data for β-peptides using Molecular Dynamics Simulations
JACS 127 (2005) 14320-14329

05.43
S.J. Marrink, H.J. Risselada and A.E. Mark
Simulation of the order-disorder transformation in lipid bilayers using a coarse grained model
Chem.Phys.Lip. 135 (2005) 223-244

05.44
A.H. de Vries, S. Yefimov, A.E. Mark and S.J. Marrink
Molecular structure of the lecithin ripple phase
PNAS 102 (2005)5392-5396

05.45
A. Pineiro, A. Villa, T. Vagt, B. Koksch, and A.E. Mark
A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: possibilieters and limitations
Biophys. J. 89 (2005) 3701-3713

05.46
S. Donnini, A.E. Mark, A. H. Juffer, A. Villa
Incorporating the Effect of Ionic Strength in Free Energy Calculations Using Explicit Ions
J. Comput. Chem. 26 (2005) 115.122

05.47
D. Kovalskyy, V. Dubyna, A.E. Mark, A. Kornelyuk
A Molecular Dynamics Study of the Structural Stability of HIV-1 Protease under Physiological Conditions: The Role of Na+ Ions in Stabilizing the Active Site
Proteins 58 (2005) 450-458

05.48
P. Soto, J. Cladera, A.E. Mark, X. Daura
Stability of SIV gp32 Fusion-Peptide Single-Layer Protofibrils as Monitored by Molecular-Dynamics Simulations
Angewandte Chemie 117 (2005) 1089-1091

05.49
V. Knecht, M. Mueller, M. Bonn, S.-J. Marrink, A.E. Mark
Simulation studies of pore and domain formation in a phospholipid monolayer
J. Chem. Phys. 122 (2005) online: DOI: 10.1063/1.1825992; (Art. No. 024704)

05.50
K. Pagel, K. Seeger, B. Seiwert, A. Villa, A.E. Mark, S. Berger, B. Koksch
Advanced approaches for the characterization of a /de novo/ designed antiparallel coiled coil peptide
Org. Biomol. Chem. 3 (2005) 1189-1194

05.51
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, H.J.C. Berendsen
GROMACS: Fast, Flexible, and Free
J. Comput. Chem. 26 (2005) 1701-1718

05.52
H. Fan, A.E. Mark, J. Zhu, B. Honig
Comparative study of generalized Born models
PNAS 102 (2005) 6760-6764

05.53
M. Schenk, B. Smit, T.L.M. Maesen, T.J.H. Vlugt
Molecular simulations of the adsorption of cycloalkanes in MFI-Type silica
Phys. Chem. Chem. Phys. 7 (2005) 2622-2628

2006

06.01
P.J. Gee and W.F. van Gunsteren
Numerical simulation of the effect of solvent viscosity on the motions of a β-peptide heptamer
Chem. Eur. J. 12 (2006) 72-75

06.02
P.J. Gee and W.F. van Gunsteren
Acetonitrile revisited: a molecular dynamics study of the liquid phase
Molecular Physics 104 (2006) 477-483

06.03
I. Chandrasekhar, W.F. van Gunsteren, G. Zandomeneghi, P.T.F. Williamson and B. Meier
Orientation and Conformational Preference of Leucine-Enkephalin at the Surface of a Hydrated Dimyristoylphosphatidylcholine Bilayer: NMR and MD Simulation
JACS 128 (2006) 159-170 and suppl. material

06.04
P.J. Gee and W.F. van Gunsteren
Terminal-group effects on the folding behaviour of selected β-peptides
Proteins 63 (2006) 136-143

06.05
B. Zagrovic and W. F. van Gunsteren
Comparing atomistic simulation data with the NMR experiment: How much can NOE's actually tell us?
Proteins 63 (2006) 210-218

06.06
D.P. Geerke and W.F. van Gunsteren
Force Field Evaluation for Biomolecular Simulation: Free Enthalpies of Solvation of Polar and Apolar Compounds in Various Solvents
ChemPhysChem 7 (2006) 671-678

06.07
Y. Zhou, C. Oostenbrink, A. Jongejan, W.F. van Gunsteren, W.R. Hagen, S.W. de Leeuw, J.A. Jongejan
Computational study of ground state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations
J. Comput. Chem. 27 (2006) 857-867

06.08
P.J. Gee and W.F. van Gunsteren
Numerical simulation of the pressure-denaturation of a helical β-peptide heptamer solvated in methanol
Helv. Chim. Acta 89 (2006) 475-482

06.09
M.A. Cuendet
Statistical mechanical derivation of the Jarzynski identity for non-Hamiltonian thermostated dynamics
Phys. Rev. Lett. 96 (2006) 120602 on-line

06.10
M.A. Kastenholz and P.H. Hünenberger
Computation of methodology-independent ionic solvation free energies from molecular simulations: I. The electrostatic potential in molecular liquids
J. Chem. Phys. 124 (2006)

06.11
M.A. Kastenholz and P.H. Hünenberger
Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations: A continuum-electrostatics study
J. Chem. Phys. 124 (2006)

06.12
R. Baron, A.H. de Vries, P.H. Hünenberger, W.F. van Gunsteren
A Comparison of Atomic-Level and Coarse-Grained Models for Liquid Hydrocarbons from Molecular Dynamics Configurational Entropy Estimates
J. Phys. Chem. B 110 (2006) 8464-8473

06.13
C. S. Pereira, D. Kony, R. Baron, M. Müller, W.F. van Gunsteren, P.H. Hünenberger
Conformational and dynamical properties of disaccharides in water: a molecular dynamics study
Biophys. J. 90 (2006) 4337-4344

06.14
V. Kräutler and P.H. Hünenberger
A multiple-timestep algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the timestep size for the fast evaluation of non-bonded interactions in molecular simulations
J. Comput. Chem. 27 (2006) 1163-1176

06.15
M.A. Kastenholz and P.H. Hünenberger
Computation of methodology-independent ionic solvation free energies from molecular simulations: II. The hydration free energy of the sodium cation
J. Chem. Phys. 124 (2006) on-line (DOI: 10.1063/1.2201698)

06.16
W.F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, D.P. Geerke, A. Glättli, P.H. Hünenberger, M.A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N.F.A. van der Vegt and H.B. Yu
Biomolecular modelling: goals, problems, perspectives
Angew. Chem 118 (2006) 4168-4198
Angew. Chem. Int. Ed. 45 (2006) 4064-4092

06.17
J. Dolenc, R. Baron, C. Oostenbrink, J. Koller and W.F. vanGunsteren
Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding
Biophysical Journal 91 (2006) 1460-1470

06.18
R. Baron, A.H. de Vries, P.H. Hünenberger and W.F. van Gunsteren
Configurational entropies of lipids in pure and mixed bilayers from atomic level and coarse-grained molecular dynamics simulations
J. Phys. Chem. B 110 (2006) 15602-15614 and suppl. material

06.19
D. Seebach, D. F. Hook, A. Glättli
Helices and Other Secondary Structures of β- and γ-Peptides
Biopolymers 84 (2006) 23-37

06.20
N.F.A. van der Vegt, M.-E. Lee, D. Trzesniak, W.F. van Gunsteren
Enthalpy-entropy compensation in the effects of urea on hydrophobic interactions
J. Phys. Chem. B 110 (2006) 12852-12855

06.21
C.S. Pereira and P.H. Hünenberger
Interaction of the sugars trehalose, maltose and glucose with a phopholipid bilayer: a comparative molecular dynamics study
J.Phys.Chem. B 110 (2006) 15572-15581 and suppl. material

06.22
H. Yu, D.P. Geerke, H. Liu and W.F. van Gunsteren
Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models
J. Comput. Chem. 27 (2006) 1494-1504

06.23
R.Baron
Biomolecular simulation: calculation of entropy and free energy, polypeptide and carbopeptoid folding, simplification of the force field for lipid simulations.
Thesis Nr. 16584, ETH Zürich, 2006

06.24
M. Christen
Algorithms and software for efficient biomolecular simulation
Thesis Nr. 16564, ETH Zürich, 2006

06.25
M. Christen, A.-P.E. Kunz, W.F. van Gunsteren
Sampling of rare events using hidden restraints
J. Phys. Chem. B 110 (2006) 8488-8498

06.26
D. Trzesniak, R.D. Lins, W.F. van Gunsteren
A protein under pressure: Molecular dynamics simulation of the Arc repressor
Proteins 65 (2006) 136-144

06.27
V. Kräutler
Classical Molecular Dynamics Simulation: Contributions to Methodology Development and Applicaitons to Biomolecular Systems
Thesis Nr. 16662, ETH Zürich, 2006

06.28
M. Christen and W.F. van Gunsteren
Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems
J. Chem. Phys. 124 154106 (2006) (7 pages) on-line (DOI: 10.1063/1.2187488)

06.29
M.A. Kastenholz, T.U. Schwartz, P.H. Hünenberger
The Transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation
Biophys. J. 91 (2006) 2976-2990

06.30
M.A. Cuendet
The Jarzynski identity derived from general Hamiltonian or non-Hamiltonian dynamics reproducing NVT or NPT ensembles
J. Chem. Phys. 125 (2006) 144109 (DOI: 10.1063/1.2338535)

06.31
D. Trzesniak, W.F. van Gunsteren
Pathway dependence of the efficiency of calculating free energy and entropy of solute-solute association in water
Chem. Phys. 330 (2006) 410-416 (DOI:10.1016/j.chemphys.2006.09.012)

06.32
D. Trzesniak
Interplay between computer simulations and experimental data in physical chemistry and structural biology: testing, interpretation and prediction
Thesis Nr. 16661, ETH Zürich, 2006

06.33
D. Trzesniak, A.-P.E. Kunz, W.F. van Gunsteren
A comparison of methods to compute a potential of mean force
ChemPhysChem 8 (2007) 162-169 (DOI: 10.1002/cphc.200600527)

06.34
D. Trzesniak, B. Jaun, R.I. Mathad, W.F. van Gunsteren
Simulation of an all-β3-icosapeptide containing the twenty proteinogenic side chains: effect of termperature, pH, counterions, solvent and force field on helix stability
Biopolymers 83 (2006) 636-645 and supporting mat. on-line DOI:10.1002/bip.20601

06.35
T. Heinz
Computer simulation of molecular systems: new algorithms and selected applications
Thesis Nr. 16608, ETH Zürich, 2006

06.36
M.A. Cuendet
Aspects of thermostated and nonautonomous molecular dynamics
Thesis Nr. 16863, ETH Zürich, 2006

06.37
H. Yu, A. Kohl, H.K. Binz, A. Plückthun, M.G. Grütter and W.F. van Gunsteren
Molecular Dynamics Study of the Stabilities of Consensus Designed Ankyrin Repeat Proteins
Proteins 65 (2006) 285-295

06.38
D. Trzesniak, W.F. van Gunsteren
Catalytic mechanism of Cyclophilin as observed in molecular dynamics simulations: pathway prediction and reconciliation of X-ray crystallographic and NMR solution data
Prot. Sci. 11 (2006) 2544-2551 and supporting mat.

06.39
A. Villa, A.E. Mark, G.A.A. Saracino, U. Cosentino, D. Pitea, G. Moro, M. Salmona
Conformational polymorphism of the PrP106-126 peptide in different environments: A molecular dynamics study
J. Phys. Chem. B 110 (2006) 1423-1428

06.40
T.A. Wassenaar, A.E. Mark
The effect of Box shape on the dynamic properties of proteins simulated under periodic boundary conditions
J. Comput. Chem. 27 (2006) 316-325

06.41
V. Knecht, A.E. Mark, S.-J. Marrink
Phase Behavior of a Phospholipid/Fatty Acid/Water Mixture Studied in Atomic Detail
JACS 128 (2006) 2030-2034

06.42
H. Fan, A.E. Mark
Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures
Protein Science 15 (2006) 441-448

06.43
H. Fan, X. Wang, J. Zhu, G.T. Robillard, A.E. Mark
Molecular Dynamics Simulations of the Hydrophobin SC3 at a Hydrophobic/Hydrophilic Interface
Proteins 64 (2006) 863-873

06.44
D.P. Tieleman, S.-J. Marrink
Lipids Out of Equilibrium: Energetics of Desorption and Pore Mediated Flip-Flop
JACS 128 (2006) 12462-12467

06.45
H. Leontiadou, A.E. Mark, S.-J. Marrink
Antimicrobial Peptides in Action
JACS 128 (2006) 12156-12161

06.46
T. Kampmann, D.S. Mueller, A.E. Mark, P. R. Young, B. Kobe
The Role of Histidine Residues in Low-pH-Mediated Viral Membrane Fusion
Structure 14 (2006) 1481-1487

06.47
L. Smith, R.J. Davies and W.F. van Gunsteren
Molecular dynamics simulations of Hydrogenobacter thermophilus
cytochrome c552 ; Comparisons of the wild type protein, a beta-type
variant and the Apo state
Proteins 65 (2006) 702-711

06.48
R. Baron, W.F. van Gunsteren and P.H. Hünenberger
Estimating the configurational entropy from molecular dynamics simulations: anharmonicity and correlation corrections to the quasi-harmonic approximation
Trends in Physical Chemistry 11 (2006) 87-122

2007

07.01
B. Keller, M. Christen, C. Oostenbrink and W.F. van Gunsteren
On using oscillating time-dependent restraints in MD simulation
J. Biomol. NMR 37 (2007) 1-14

07.02
C. Oostenbrink, M.M.H. van Lipzig and W.F. van Gunsteren
Applications of molecular dynamics simulations in drug design, in "Comprehensive Medicinal Chemistry II" Vol. 4, Computer-Assisted Drug Design,
J.B. Taylor and D.J. Triggle Eds., Elsevier, Amsterdam, 2007, 651-668

07.03
R. Baron, D. Trzesniak, A.H. de Vries, A. Elsener, S.J. Marrink, W.F. van Gunsteren
Comparison of thermodynamic properties of Coarse-grained and atomic-level simulaton models
ChemPhysChem 8 (2007) 452 - 461

07.04
B. Zagrovic, W.F. van Gunsteren
Computational analysis of the mechanism and thermodynamics of inhibition of phosphodiesterase 5A by synthetic ligands
J. Chem. Theory Comput. 3 (2007) 301-311, incl. supp. material

07.05
Z. Gattin, A. Glättli, B. Jaun, W.F. van Gunsteren
Simulation of β-depsipeptides: The effect of missing hydrogen-bond donors on their folding equilibria
Biopolymers 85 (2007) 318-332, incl. supp. mat.

07.06
D. Trzesniak, N.F.A. van der Vegt, W.F. van Gunsteren
Analysis of neo-pentane-urea pair potentials of mean force in aqueous urea
Mol. Phys. 105 (2007) 33-39

07.07
M. E. Siwko, S.J. Marrink, A.H. de Vries, A. Kozubek, A.J.M. Schoot Uiterkamp, A.E. Mark
Does isoprene protect plant membranes from thermal shock? A molecular dynamics study
Biochimica et Biophysica Acta 1768 (2007) 198-206

07.08
X. Periole, A.E. Mark
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
J. Chem. Phys. 126 (2007) 014903 (DOI 10.1063/1.2404954, Art. No. 014903)

07.09
N. Schmid, B. Zagrovic, W.F. van Gunsteren
Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA
Biochemistry 46 (2007) 6500-6512 (DOI: 10.1021/bi60626133)

07.10
C.D. Christ, W.F. van Gunsteren
Enveloping Distribution Sampling: A method to calculate free energy differences from a single simulation
J. Chem. Phys. 126 (2007) 184110 (DOI: 10.1063/1.2730508)

07.11
D.B. Kony, P.H. Hünenberger, W.F. van Gunsteren
Molecular dynamics simulations of the native and partially-folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics
Proteins 16 (2007) 1101-1118

07.12
W.F. van Gunsteren, Z. Gattin
Simulation of folding equilibria
"Foldamers: Structure, properties and applications" S. Hecht & I. Huc eds., Wiley, Weinheim, Germany, 2007, 173-192

07.13
M. Christen, C. Christ, W.F. van Gunsteren
Free energy calculations using flexible-constrained, hard-constrained and non-constrained MD simulations
Chem.Phys.Chem. 8 (2007) 1557-1564 (DOI: 10.1002/cphc.200700176)

07.14
J.H. Missimer, M.O. Steinmetz, R. Baron, F.K. Winkler, R.A. Kammerer, X. Daura, W.F. van Gunsteren
Configurational entropy elucidates the role of salt-bridge networks in protein thermostability
Prot. Sci. 16 (2007) 1349-1359 incl. supporting material (DOI: 10.1110/ps.062542907)

07.15
M.I. El-Barghouthi, M. Schenk, M.B. Zughul, A.A. Badwan, W.F.
van Gunsteren
Comparison of estimates of free energy for binding of mono- and
di-substituted benzenes with alpha-cyclodextrin obtained by single-step
perturbation and thermodynamic integration
J. Incl. Phenom Macrocycl. Chem. 57 (2007) 375-377
(DOI:10.1007/s10847-006-9257-0)

07.16
D.B. Kony, W. Damm, S. Stoll, W.F. van Gunsteren, P.H. Hünenberger
Explicit-solvent molecular dynamics simulations of the
polysaccharide schizophyllan in water
Biophys. J. 93 (2007) 442-455 (DOI:10.1529/biophysj.106.086116)

07.17
E.S. Leite, S.R. Santana, P.H. Hünenberger, L.C.G. Feitas, R.L. Longo
On the relative stabilities of the alkaly cations 222 cryptates in the
gas phase and in water-methanol solution
J. Mol. Modl. 13 (2007) 1017-1025 (DOI: 10.1007/s00894-007-0213-8)

07.18
V. Kräutler, M. Müller, P.H. Hünenberger
Conformation, dynamics, solvation and relative stabilities of selected
beta-hexopyranoses in water: a molecular dynamics study with the GROMOS
45A4 force field.
Carbohydr. Res. 342 (2007) 2097-2124, incl. supp. material

07.19
M. Christen, W.F. van Gunsteren
On searching in, sampling of, and dynamically moving through
conformational space of biomolecular systems: a review
J. Comput. Chem. 29 (2007) 157-166 (DOI: 10.1002/jcc.20725)

07.20
D. Bakowies
Extrapolation of electron correlation energies to finite and complete basis set targets
J. Chem. Phys 127 (2007) incl. supp. mat. (DOI:10.1063/1.2749516)

07.21
D.P. Geerke, W.F. van Gunsteren
The performance of non‐polarizable and polarizable force‐field parameter stets for ethylene glycol in molecular dynamics simulation of the pure liquid and its aqueous mixtures
Mol. Phys. 105 (2007) 1861–1881

07.22
W. F. van Gunsteren, D.P. Geerke, C. Oostenbrink, D. Trzesniak, N. F. A. van der Vegt
Analysis of the driving forces for biomolecular solvation and association In: ʺProtein Folding and Drug Designʺ, Proceedings of the International School of Physics ʺEnrico Fermiʺ, course CLXV, R.A. Broglia, L. Serrano and G. Tiana, eds., IOS Press, Amsterdam – SIF, Bologna (2007), pages 177‐191

07.23
D. Bakowies
Accurate extrapolation of electron correlation energies from small basis sets
J. Chem. Phys. 127 (2007) 164109, incl. supp. mat.

07.24
N. Schmid, B. Zagrovic, W.F. van Gunsteren
Folding‐unfolding equilibrium of a methylene substituted beta‐peptide
Helv. Chem. Acta 90 (2007) 1966‐1979

07.25
D.P. Geerke, St. Thiel, W. Thiel, W.F. van Gunsteren
QM‐MM Interactions in Simulations of Liquid Water using Combined Semi‐Empirical/Classical Hamiltonians
Phys. Chem. Chem. Phys. 10 (2008) 297‐302 (DOI: 10.1039/b713197f)

07.26
D.P. Geerke, W.F. van Gunsteren
On the calculation of atomic forces in classical simulation using the charge‐on‐spring method to explicitly treat electronic polarisation
J. Chem. Theory Comput. 3 (2007) 2128-2137 (DOI: 10.1021/ct700164k)

07.27
M.A. Cuendet, W.F. van Gunsteren
On the calculation of velocity-dependent properties in molecular dynamics simulations using the leap-frog integration algorithm
J. Chem. Phys. 127 (2007) 184102 (DOI: 10.1063/1.2779878)

07.28
D.P. Geerke, St. Thiel, W. Thiel, W. F. van Gunsteren
A combined QM/MM molecular dynamics study on a condensed‐phase SN2 reaction at saturated nitrogen: the effect of explicitly including solvent polarization
J. Chem. Theory Comput. 3 (2007) 1499-1509 (DOI: 10.1021/ct7000123)

07.29
M. Christen, B. Keller and W.F. van Gunsteren
Biomolecular structure refinement based on adaptive restraints using local‐elevation simulation
J. Biomol. NMR 39 (2007) 265‐273 (DOI: 10.1007/s10858‐007‐9194‐2)

07.30
D. Geerke
Classical Hamiltonians in molecular simulation: force‐field development and explicit inclusion of electronic polarization and quantum effects
Thesis Nr. 17348, ETH Zurich, 2007

07.31
M. Winger, H. Yu, Ch. Redfield, W.F. van Gunsteren
Molecular dynamics simulation of human interleukin‐4: comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability
Mol. Simulation 33 (2007) 1143‐1154

07.32
B. Zagrovic
Helical signature motif in the fiber diffraction patterns of random‐walk chains
Mol. Phys. 105 (2007) 1299‐1306

07.33
S. Takahashi, H. Satoh, Y. Hongo, H. Koshino
Structural Revision of Terpenoids with a (3Z)‐2‐Methyl‐3‐penten‐2‐ol Moiety by the Synthesis of (23E)‐ and (23Z)‐Cycloart‐23‐ene‐3β,25‐diols”
J. Org. Chem. 72 (2007) 4578‐4581

07.34
H. Satoh
Numerical Representation of Stereochemical Environments by Using FRAU
Croatica Chimica Acta 80 (2007) 217‐225

07.35
S. Koichi, S. Iwata, T. Uno, H. Koshino, H. Satoh
Algorithm for Advanced Canonical Coding of Planar Chemical Structures That Considers Stereochemical and Symmetric Information
J. Chem. Inf. Model. 47 (2007) 1734‐1746

07.36
A. Elsener, C.C.M. Samson, M.P. Brändle, P. Bühlmann, H.P. Lüthi
Statistical Analysis of Quantum Chemical Data Using Generalized XML/CML Archives for the Derivation of Molecular Design Rules
Chimia 61 (2007) 165–168

07.37
D.P. Geerke, W.F. van Gunsteren
Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters
J. Phys. Chem. B 111 (2007) 6425-6436

07.38
M. Terzer, M. Jovanovic, A. Choutko, O. Nikolayeva, A. Korn, D. Brockhoff, F. Zürcher, M. Friedmann, R. Schütz, E. Zitzler, J. Stelling, S. Panke
Design of a biological half adder
IET Synth.Biol 1 (2007) 53-58

2008

08.01
M.O. Steinmetz, Z. Gattin, R. Verel, B. Ciani, T. Stromer, J.M. Green, P. Tittmann, C. Schultze-Brise, H. Gross, W.F. van Gunsteren, B.H. Meier, L.C. Serpell, S.A. Müller, R. Kammerer
Atomic model of de novo designed ccβ-Met amyloid-like fibrils
J. Mol. Biol. 376 (2008) 898-912

08.02
Z. Gattin and W.F. van Gunsteren
A molecular dynamics study of the ASC and NALP1 Pyrin domains at neutral and low pH
ChemBioChem 9 (2008) 923-933

08.03
R. Boned, W.F. van Gunsteren, X. Daura
Estimating the temperature dependence of peptide-folding entropies and free enthalpies from total
energies in molecular dynamics simulations
Chem.Eur.J. 14 (2008) 5039-5046, DOI: 10.1002/chem.200701380

08.04
W.F. van Gunsteren, J. Dolenc
Biomolecular simulation: historical picture and future perspectives
Biochem. Soc. Trans. 36 (2008) 11-15, DOI:10.1042/BST0360011

08.05
W.F. van Gunsteren, J.Dolenc, A.E. Mark
Molecular simulation as an aid to experimentalists
Curr. Opin. Struct. Biology 18 (2008) 149-153, DOI: 10.1016/j.sbi.2007.12.007

08.06
B. Zagrovic, Z. Gattin, J. Kai-Chi Lau, M. Huber, W.F. van Gunsteren
Structure and dynamics of two β-peptides in solution from molecular
dynamics simulations validated against experiment
Eur. Biophys. J. (2008) 37 (2008), 903-912

08.07
P.A. Limacher, H.P. Lüthi
2.3-Diphenylbutadiene and donor-acceptor functionalized derivatives:
Exploring the competition between conjugation paths in branched pi-systems
J. Phys. Chem. A 112 (2008) 2913-2919

08.08
C.D. Christ, W.F. van Gunsteren
Multiple free energies from
a single simulation: Extending enveloping distribution sampling to
non-overlapping phase-space distributions
J. Chem. Phys. 128 (2008) 174112, DOI:10.1063/1.293050

08.09
J. Dolenc, R. Baron, J.H. Missimer, M.O. Steinmetz, W.F. van Gunsteren
Exploring the conserved water sites and hydration of a coiled-coil trimerization motif: a MD simulation study
ChemBioChem. 9 (2008) 1749-1756, DOI: 10.1002/cbic.200800096

08.10
V. Kräutler, P.H. Hünenberger
Explicit-solvent molecular
dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum
versus reaction-field electrostatics
Mol. Sim. 34 (2008) 491-499

08.11
T. Todorova, P.H. Hünenberger, J. Hutter
Car-Parrinello molecular dynamics simulation of CaCl2 aqueous solutions
J. Chem. Theory Comput. 4 (2008) 779-789

08.12
L. Peric, C.S. Pereira, S. Pérez, P.H. Hünenberger
Conformation, dynamics and ion-binding properties of single-chain polyuronates: a molecular dynamics study
Mol. Simul. 34 (2008) 421-446 incl. suppl. mat

08.13
C.S. Pereira, P.H. Hünenberger
The influence of polyhydroxylated compounds on a hydrated phospholipid bilayer: a molecular dynamics study
Mol. Simul. 34 (2008) 403-420

08.14
W.F. van Gunsteren and D.P. Geerke
Computer simulation of biomolecular systems: Where do we stand?
In: "From Computational Biophysiscs to System Biology (CBSB08)", Proceedings John von Neumann Institute for Computing (NIC), Vol. 40, U.H.E. Hansmann, J.H. Meinke, S. Mohanty, W. Nadler, O.Zimmermann, eds., (2008), Jülich, Germany, pp. 49-55

08.15
A. Choutko, A. Glättli, W.F. van Gunsteren
Simulation of the outer membrane protein X in a lipid bilayer and in a micelle
In: "From Computational Biophysiscs to System Biology (CBSB08)",
Proceedings John von Neumann Institute for Computing (NIC), Vol. 40,
U.H.E. Hansmann, J.H. Meinke, S. Mohanty, W. Nadler, O.Zimmermann,
eds., (2008), Jülich, Germany, pp. 181-184

08.16
D.P. Geerke, S. Luber, K.H. Marti, W.F. van Gunsteren
On the direct calculation of the free energy of quantisation for molecular systems in the condensed phase
J. Comput. Chem. 4 (2008) 514-523, DOI: 10.1002/jcc.21070

08.17
F. Schwab, W.F. van Gunsteren, B. Zagrovic
Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalene-hopene cyclase
Biochem. 47 (2008) 2945-2951, incl. supp. mat.

08.18
C.S. Pereira, P.H. Hünenberger
The effect of trehalose on a phospholipid membrane under mechanical stress
Biophys. J. 95 (2008) 3525-3534

08.19
M. Winger, W.F. van Gunsteren
Use of molecular dynamics simulation for optimising protein stability: Consensus designed ankyrin repeat proteins
Helv. Chim. Acta 91 (2008) 1605-1613

08.20
N. Schmid, Ch. Bolliger, L.J. Smith, W.F. van Gunsteren
Disulfide bond shuffling in bovine alpha-lactalbumin: MD simulation confirms experiment
Biochemistry 47 (2008)12104-12107, DOI: 10.1021/bi8013455

08.21
Z. Gattin
Computer simulations of peptides and proteins: a comparison of effects of solute and solvent variation upon simulated and measured observables
Diss. ETH No. 17954

08.22
M. Winger
Classical molecular dynamics simulations at different levels of resolution: force field development and applications
Diss. ETH No. 18076

2009

09.01
C.D. Christ, W.F. van Gunsteren
Simple, efficient, and reliable computation of multiple free energy differences from a single simulation: a reference Hamiltonian parameter update scheme for enveloping distribution sampling (EDS)
J.Chem.Theory Comput. 5 (2009) 276–286, DOI: 10.1021/ct800424v

09.02
M. Winger, D. Trzesniak, R. Baron, W.F. van Gunsteren
On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models
Phys. Chem. Chem. Phys. 11 (2009) 1934-1941, DOI: 10.1039/b818713d

09.03
H. Satoh, J. Hutter, H.P. Lüthi, S. Manabe, K. Ishii, Y. Ito
Low barrier pathway for endo-cleavage induced anomerization of pyranosides with N-benzyl-2,3-trans Oxazolidinone groups
Eur. J. Org. Chem. (2009) 1127-1131, DOI: 10.1002/ejoc.200801140

09.04
M. Bruschi, P.A, Limacher, J. Hutter, H.P. Lüthi
A scheme for the evaluation of electron delocalization and conjugation efficiency in linearly π–conjugated systems
J.Chem.Theory.Comput. 5 (2009) 506-514

09.05
D. Bakowies
Ab initio thermochemistry using optimal-balance models with isodesmic corrections: the ATOMIC protocol
J.Chem.Phys. 130, 144113 (2009); DOI:10.1063/1.3089241

09.06
M.M. Reif, V. Kräutler, M.A. Kastenholz, X. Daura, P.H. Hünenberber
Molecular dynamics simulations of a reversibly-folding beta-heptapeptide in methanol: Influence of the treatment of long-range electrostatic interactions.
J.Phys.Chem. B 113 (2008) 3112-3128

09.07
Z. Gattin, J. Schwartz, R.I. Mathad, B. Jaun, W.F. van Gunsteren
Interpreting experimental data by using molecular simulation instead of model building
Chem. Eur. J. 15 (2009) 6389 – 6398, DOI: 10.1002/chem.200802523, incl. suppl. mat.

09.08
Z. Gattin, W.F. van Gunsteren
Influence of backbone fluorine substitution upon the folding equilibrium of a beta-heptapeptide
J. Phys. Chem. B 113 (2009) 8695–8703, DOI: 10.1021/jp811106e

09.09
A. Lange, Z. Gattin, H. Van Melckbeke, Ch. Wasmer, A. Soragni, W.F. van Gunsteren, B.H. Meier
A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformation
ChemBioChem 10 (2009) 1657-1665, DOI: 10.1002/cbic.200900019, incl. suppl. mat.

09.10
M. Winger, M. Christen, W.F. van Gunsteren
On the conformational properties of amylose and cellulose oligomers in solution
Int. J. Carbohydr. Chem. (2009) 1-8, DOI:10.1155/2009/307695

09.11
M. Winger, A.H. de Vries, W.F. van Gunsteren
Force-field dependence of the conformational properties of α, ω-dimethoxypolyethylene glycol
Mol. Phys. 107 (2009) 1313-1321

09.12
D. Wang, B. Jaun, W.F. van Gunsteren
Folding and unfolding of two mixed alpha/beta peptides
ChemBioChem. 10 (2009) 2032-2041, DOI: 10.1002/cbic.200900125

09.13
C.L. Müller, I.F. Sbalzarini, W.F. van Gunsteren, B. Zagrovic, P. Hünenberger
In the eye of the beholder: inhomogeneous distribution of high-resolution shapes within the random-walk ensemble
J. Chem. Phys. 130 (2009) 214904

09.14
A.P. Kunz, W.F. van Gunsteren
Development of a non-linear classical polarisation model for liquid water and aqueous solutions: COS/D
J. Phys. Chem. A 113 (2009) 11570-11579 DOI: 10.1021/jp903164s

09.15
C.D. Christ, W.F. van Gunsteren
Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation
J. Comput. Chem. 30 (2009) 1664-1679

09.16
Z. Gattin, S.Riniker, P.J. Hore, K.H. Mok, W.F. van Gunsteren
Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: a simulation study consistent with experimental observations
Prot. Sci. 18 (2009) 2090-2099, DOI: 10.1002/pro.223

09.17
J.R. Allison, W.F. van Gunsteren
A method to explore protein side chain conformational variability using experimental data
ChemPhysChem 10 (2009) 3213-3228, DOI: 10.1002/cphc.200900400

09.18
D. Bakowies
Ab initio thermochemistry with high-level computed isodesmic corrections: Validation of the ATOMIC protocol for a large set of compounds with first-row atoms (H, C, N, O, F)
J. Phys. Chem. A 113 (2009) 11517-11534

09.19
H.S. Hansen, P.H. Hünenberger
Using the local elevation method to construct optimized umbrella sampling potentials: calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water
J. Comput. Chem. 31 (2010) 1-23, DOI 10.1002/jcc.21253

09.20
C.A. Lopez, A. Rzepiela, A.H. de Vries, P.H. Hünenberger, S.J. Marrink
The Martini coarse grained force field: extension to carbohydrates
J. Chem. Theory Comput. 5 (2009) 3195-3210, incl. suppl. mat.

09.21
R. Baron, P.H. Hünenberger, J.A. McCammon
Absolute single-molecule entropies from quasi-harmonic analysis of microsecond molecular dynamics: correction terms and convergence properties
J. Chem. Theory Comput. 5 (2009) 3150-3160, incl. suppl. mat.

09.22
K.H. Hughes, C.D. Christ, I. Burghardt
Effective-mode representation of non-Markovian dynamics: A hierarchical approximation of the spectral density. I. Application to single surface dynamics
J. Chem. Phys. 131 (2009) 024109, DOI:10.1063/1.3159671

09.23
B. Vögeli, T.F. Segawa, D. Leitz, A. Sobol, A. Choutko, D. Trzesniak, W.F. van Gunsteren, R. Riek
Exact distances and internal dynamics of ubiquitin from NOE buildups
J. Am. Chem. Soc. 131 (2009) 17215-17225, DOI: 10.1021/ja905366h

09.24
D. Poger, W.F. van Gunsteren, A.E. Mark
A new force field for simulating phosphatidylcholine bilayers
J. Comput. Chem. 31 (2010) 1117-1125, DOI 10.1002/jcc.21396

09.25
P.A. Limacher, K.V. Mikkelsen, H.P. Lüthi
On the accurate calculation of polarizabilities and second hpyerpolarizabilities of poyacetylene oligomer chains using the CAM-B3LYP density functional
J. Chem. Phys. 130 (2009) 194114, DOI: 10.1063/1.3139023

09.26
S. Borini, P.A. Limacher, H.P. Lüthi
A systematic analysis of the structure and (hyper)polarizability of donor-acceptor substituted polyacetylenes using a Coulomb-attenuating density functional
J. Chem. Phys. 131 (2009), 124105, DOI: 10.1063/1.3216825

09.27
K.H. Hughes, C.D. Christ, I. Burghardt
Effective-mode representation of non-Markovian dynamics: A hierarchical approximation of the spectral density. lI. Application to environment-induced nonadiabatic dynamics
J. Chem. Phys. 131 (2009) on-line, DOI:10.1063/1.3226343

09.28
C.D. Christ, A.E. Mark, W.F. van Gunsteren
Basic ingredients of free energy calculations: a review
J. Comput. Chem. 31 (2010) 1569-1582, DOI: 10.1002/jcc.21450

09.29
X. Periole, M. Cavalli, S.J. Marrink, M. Ceruso
Combining an elastic network with a coarse-grained molecular force field: structure, dynamics and intermolecular recognition
Journal of Chemical Theory and Computation 5 (2009) 2531-2543

09.30
D. Sengupta, A. Rampioni, S. J. Marrink
Simulations of the C-subunit of ATP-Synthase Reveal Helix Rearrangements
Molecular Membrane Biology 26 (2009) 422-434

09.31
H.J. Risselada, S.J. Marrink
The freezing process of small lipid vesicels at molecular resolution
Soft Matter 5 (2009) 4531-4541

09.33
M.J. Hinner, S.J. Marrink, A.H. de Vries.
Location, tilt, and binding: a molecular dynamics study of voltage sensitve dyes in biomembranes
J. Phys. Chem. B 113 (2009) 15807-15819

2010

10.01
K. Meier, W.F. van Gunsteren
A cyclic beta-helical / beta-hairpin D, L-alpha-peptide: study of its folding properties and structure refinement using molecular dynamics
J. Phys. Chem. A 114 (2010) 1852-1859, DOI: 10.1021/jp906218f

10.02
W.F. van Gunsteren, M. Winger
Reply to the comment on using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models
Phys. Chem. Chem. Phys. 12 (2010) 2257-2258, DOI: 10.1039/b922516c

10.03
B. Keller, Z. Gattin, W.F. van Gunsteren
What stabilizes the 3₁₄-helix in beta³-peptides? A conformational analysis using molecular simulation
Proteins 78 (2010) 1677-1690, DOI: 10.1002/prot.22685

10.04
B. Keller, X. Daura, W.F. van Gunsteren
Comparing geometric and kinetic cluster algorithms for molecular simulation data
J. Chem. Phys. 132 (2010) 074110, DOI:10.1063/1.3301140

10.05
Z. Gattin, J. Zaugg, W.F. van Gunsteren
Structure Determination of a Flexible Cyclic Peptide Based on NMR and MD Simulation ³J-Coupling
Chem. Phys. Chem 11 (2010) 830-835, DOI: 10.1002/cphc.200900501

10.06
N. Schmid, M. Bötschi, W.F. van Gunsteren
A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software
J. Comput. Chem. 31 (2010) 1636-1643, DOI 10.1002/jcc

10.07
S. Borini, P.A. Limacher, H.P. Lüthi
Structural Features Analysis and Nonlinearity of End-Cap-Substituted Polyacetylenes
J. Phys. Chem. A 114 (2010) 2221-2229, DOI: 10.1063/1.3216825

10.08
Z. Lin, H. Liu, W.F. van Gunsteren
Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a beta-peptide in solution
J. Comput. Chem. 31 (2010) 2419-2427, DOI: 10.1002/jcc.21534, incl. supp. mat.

10.09
Z. Lin, J.Kornfeld, M. Mächler, W.F. van Gunsteren
Prediction of folding equilibria of differently substituted peptides using one-step perturbation
J. Am. Chem. Soc. 132 (2010) 7226-7278, DOI: 10.1021/ja100879k, incl. supp. mat.

10.10
H. Satoh, H. Hansen, S. Manabe, P.H Hünenberger, W.F. van Gunsteren
Theoretical Investigation of Solvent Effects on Glycosylation Reactions: Stereoselectivity Controlled by Preferential Conformations of the Intermediate Oxocarbonium - Counterion Complex
J. Chem. Theory Comput. 6 (2010) 1783-1797, DOI: 10.1021/ct1001347, incl. supp. mat.

10.11
D. Wang, M. Friedmann, Z. Gattin, B. Jaun, W.F. van Gunsteren
The propensity of aminoisobutyric acid (Aib) to induce helical secondary structure in an beta-heptapeptide: a computational study
Helv. Chim. Acta 93 (2010) 1513-1531, DOI: 10.1002/hlca.200900420

10.12
D. Wang, T. Merz, W.F. van Gunsteren
The thermal isomerization of the GFP chromophore: a computational study
Phys. Chem. Chem. Phys. 36 (2010) 11051-11061, DOI: 10.1039/C0CP00181C

10.13
A.P. Eichenberger, Z. Gattin, G. Yalak, W.F. van Gunsteren
Molecular dynamics simulation of ester-linked hen egg white lysozyme reveals the effect of missing backbone hydrogen-bond donors on the protein structure
Helv. Chim. Acta 93 (2010) online, DOI: 10.1002/ hlca. 201000077

10.14
J. Dolenc, J.H. Missimer, M.O. Steinmetz, W.F. van Gunsteren
Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1
J. Biomol. NMR 47 (2010) 221-235, DOI: 10.1007/s10858-010-9425-9

10.15
J.R. Allison, G.P. Moll, W.F. van Gunsteren
Investigation of stability and disulfide bond shuffling of lipid transfer proteins by molecular dynamics simulation
Biochemistry 49 (2010) 6916-6927, DOI: 10.1021/bi100383m, incl. supp. mat

10.16
L. Peric-Hassler, H.S. Hansen, R. Baron, P.H. Hünenberger
Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling
Carbohydrate Res. 345 (2010) 1781–1801, DOI: 10.1016/j.carres.2010.05.026, incl. supp. mat

10.17
J. Dolenc, S. Gerster, W.F. van Gunsteren
Molecular dynamics simulations reveal the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA
J. Phys. Chem. B 114 (2010) 11164-11172, DOI: 10.1021/jp100483f, incl. supp. mat

10.18
B.A.C. Horta, A.H. de Vries, P.H. Hünenberger
Simulating the transition between gel and liquid-crystal phases of lipid bilayers: dependence of the transition temperature on the hydration level
J. Chem. Theory Comput. 6 (2010) 2488-2500, DOI: 10.1021/ct100200w

10.19
V. Kräutler, S. Hiller, P.H. Hünenberger
Residual structure in a peptide fragment of the outer membrane protein X under denaturing conditions: a molecular dynamics study
Eur. Biophys. J. 39 (2010) 1421-1432, DOI: 10.1007/s00249-010-0596-9

10.20
Z. Lin, A.P. Kunz, W.F. van Gunsteren
A one-site polarizable model for liquid chloroform: COS/C
Mol. Phys. 108 (2010) 1749-1757, DOI: 10.1080/00268976.2010.489527

10.21
D.P. Geerke, W.F. van Gunsteren, P.H. Hünenberger
Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: preferential affinity/exclusion effects and their relevance for bioprotection
Mol. Simul. 36 (2010) 708-728, DOI: 10.1080/08927021003752804

10.22
D.F. Hansen, P. Neudecker, P. Vallurupalli, F.A.A. Mulder, L.E. Kay
Determination of Leu Side-Chain Conformations in Excited Protein States by NMR Relaxation Dispersion
J. Am. Chem. Soc. 132 (1) (2010) 42-43, DOI: 10.1021/ja909294n

10.23
R. Otten, B. Chu, K.D. Krewulak, H.J. Vogel, F.A.A. Mulder
Comprehensive and cost-effective NMR spectroscopy of methyl groups in large proteins
J. Am. Chem. Soc. 132 (2010) 2952-2960, DOI: 10.1021/ja907706a

10.24
M. Fuhrmans, B.P. Sanders, S.J. Marrink, A.H. de Vries
Effects of bundling on the properties of the SPC water model
Theor. Chem. Accounts 125 (2010) 335-344, DOI: 10.1007/s00214-009-0590-4

10.25
S. Baoukina, S.J. Marrink, D.P. Tieleman.
Lateral pressure profiles in lipid monolayers
Farad. Discuss. 144 (2010) 393-409, DOI: 10.1039/b905647e

10.26
T. Apajalahti, P. Niemela, P.N. Govindan, M. Miettinen, E. Salonen, S.J. Marrink, I. Vattulainen
Concerted diffusion of lipids in raft-like membranes
Farad. Discuss. 144 (2010) 411-430, DOI: 10.1039/b901487j

10.27
A. Rzepiela, D. Sengupta, N. Goga, S.J. Marrink
Membrane poration by antimicrobial peptides combining atomistic and coarse grained descriptions
Farad. Discuss. 144 (2010) 431-443, DOI: 10.1039/b901615e

10.28
A.J. Rzepiela, L.V. Schäfer, N. Goga, H.J. Risselada, A.H. de Vries, S.J. Marrink
Reconstruction of atomistic details from coarse grained structures
J. Comp. Chem. 31 (2010) 1333-1343, DOI: 10.1002/jcc.21415

10.29
K. Wood, D.J. Tobias, B. Kessler, F. Gabel, D. Oesterhelt, F.A.A. Mulder, G. Zaccai, M. Weik
The Low-Temperature Inflection Observed in Neutron Scattering Measurements of Proteins Is Due to Methyl Rotation: Direct Evidence Using Isotope Labeling and Molecular Dynamics Simulations
J. Am. Chem. Soc 132 (2010) 4990-4991, DOI: 10.1021/ja910502g

10.30
J.A. Lycklama a Nijeholt, M. Bulacu, S.J. Marrink, A.J.M. Driessen
Immobilization of the plug domain inside the SecY channel allows unrestricted protein translocation
J. Biol. Chem. 285 (2010) 23747-23754, DOI: 10.1074/jbc.M110.124636

10.31
S. Yesylevskyy, L.V. Schäfer, D. Sengupta, S.J. Marrink
Polarizable water model for the coarse-grained Martini force field
PLoS Comp. Biol 6 (2010) e1000810, DOI: 10.1371/ journal.pcbi.1000810

10.32
Y.G. Smirnova, S.J. Marrink, R. Lipowsky, V. Knecht
Solvent-exposed tails as pre-stalk transition states for membrane fusion
J. Am. Chem. Soc. 132 (2010) 6710-6718, DOI: 10.1021/ja910050x

10.33
F.A.A. Mulder, M. Lundqvist, R. Scheek
Nuclear Magnetic Resonance Spectroscopy Applied to (Intrinsically) Disordered Proteins in "Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation"
V. Uversky and S. Longhi (Eds.) John Wiley and Sons Ltd, New Jersey (2010)
# ISBN-10: 0470343419
# ISBN-13: 978-04703434

10.34
H. Hansen, X. Daura, P.H. Hünenberger
Enhanced conformational sampling in molecular dynamics simulations of solvated peptides: Fragment-based local elevation umbrella sampling
J. Chem. Theory Comput. 6 (2010) 2598-2621, DOI: 10.1021/ct1003059

10.35
H. Hansen, P.H. Hünenberger
Ball-and-stick local elevation umbrella sampling: molecular simulations involving enhanced sampling within conformational or alchemical subspaces of low internal dimensionalities, minimal irrelevant volumes and problem-adapted geometries
J. Chem. Theory Comput. 6 (2010) 2622-2646, DOI: 10.1021/ct1003065

10.36
L. Peric-Hassler, P.H. Hünenberger
Interaction of alginate single-chain polyguluronate segments with mono- and divalent metal cations: A comparative molecular dynamics study
Mol. Simul. 36 (2010) 778-795, DOI: 10.1080/08927021003752853

10.37
S. Bachmann, B. Jaun, W.F. van Gunsteren, D. Wang
The Effect of Fluoro Substitution upon the beta-Hairpin Fold of a -beta-Tetrapeptide in Methanol
Helv. Chim. Acta 93 (2010) 1870-1881, DOI: 10.1002/hlca.201000179

10.38
A. Choutko, A. Glättli, C. Fernández, C. Hilty, K. Wüthrich, W.F. van Gunsteren
Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle
Eur. Biophys. J. (2010) online, DOI: 10.1007/s00249-010-0626-7

10.39
B. Horta, L. Peric-Hassler, P.H. Hünenberger
Interaction of the disaccharides trehalose and gentiobiose with lipid bilayers:
A comparative molecular dynamics study
J. Mol. Graph. Model. 29 (2010) 331-346, DOI: 10.1016/j.jmgm.2010.09.013

10.40
Z. Lin, W.F. van Gunsteren
Using one step perturbation to predict the folding equilibrium of differently stereochemically substituted beta-peptides
Phys. Chem. Chem. Phys 12 (2010) 15442-15447, DOI: 10.1039/c0cp00833h

10.41
J.H. Missimer, J. Dolenc, M.O Steinmetz, W.F. van Gunsteren
Exploring the trigger sequence of the GCN4 coiled-coil: biased molecular dynamics resolves apparent inconsistencies in NMR measurements
Proteins 19 (2010) 2462-2474, DOI:10.1002/pro.528, incl. supp. mat.

10.42
H. S. Hansen
Enhanced conformational sampling in molecular dynamics simulations
Thesis Nr. 19141, ETH Zürich, 2010

10.43
S. Riniker, X. Daura, W.F. van Gunsteren
-Cyclodextrin host-guest binding: A computational study analyzing the different driving forces
Helv. Chim. Acta 93 (2010) 2318-2325 DOI: 10.1002/hlca.201000251, incl. supp. mat.

10.44
J. Allison, M. Müller, W.F. van Gunsteren
A comparison of the different helices adopted by alpha- and beta-peptides suggests different reasons for their stability
Prot. Sci. 19 (2010) 2186-2195, DOI: 10.1002/pro.504

2011

11.01
Z. Lin, N.Schmid, W.F. van Gunsteren
The effect of using a polarizable solvent model upon the folding equilibrium of different beta-peptides
Mol. Phys. 109 (2011) 493-506, DOI: 10.1080/00268976.2010.532163

11.02
A. P. E. Kunz, A. P. Eichenberger, W. F. van Gunsteren
A simple, efficient polarisable molecular model for liquid carbon tetrachloride
Mol. Phys. 109 (2011) 365-372, DOI: 10.1080/00268976.2010.533208

11.03
S. Riniker, W. F. van Gunsteren
A simple, efficient polarisable coarse-grained water model for molecular dynamics simulations
J. Chem. Phys. 134 (2011) 084110, DOI: 10.1063/1.3553378

11.04
Z. Lin, F.H. Hodel, W.F. van Gunsteren
Influence of variation of a side chain in the folding equilibrium of a beta-peptide
Helv. Chim. Acta. 94 (2011) 597-610, DOI: 10.1002/hlca.201100003, incl. supp. mat.

11.05
H. Hansen, P.H. Hünenberger
A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers and glycosidic linkage conformers
J. Comput. Chem. 32 (2011) 998-1032, DOI: 10.1002/jcc.21675

11.06
B. Keller, P.H. Hünenberger, W.F. van Gunsteren
An analysis of the validity of Markov state models for emulating the dynamics of classical molecular systems and ensembles
J. Chem. Theory Comput. 7 (2011) 1032-1044, DOI: 10.1021/ct200069c

11.07
J.R. Allison, K. Boguslawski, F. Fraternali, W.F. van Gunsteren
A refined, efficient mean solvation force model that includes the interior volume contribution
J. Phys. Chem. B 115 (2011) 4547-4557, DOI: 10.1021/jp2017117, incl. supp. mat.

11.08
B. A. C. Horta, P.F.J. Fuchs, W.F. van Gunsteren, P.H. Hünenberger
New interaction parameters for oxygen compounds in the GROMOS force field: improved pure-liquid and solvation properties for alcohols, ethers, aldehydes, ketones, carboxylic acids and esters
J. Chem. Theory Comput. 7 (2011) 1016-1031, DOI: 10.1021/ct200069c

11.09
A. P. E. Kunz, W. F. van Gunsteren
Enhancing the configurational sampling of ions in aqueous solution using adiabatic decoupling with translational temperature scaling
J. Phys. Chem. B 115 (2011) 2931-2936, DOI: 10.1021/jp110778k

11.10
M. Reif, P.H. Hünenberger
Computation of methodology-independent single-ion solvation properties from molecular simulations III. Correction terms for the solvation free energies, enthalpies, entropies heat capacities, volumes, compressibilities and expansibilities of solvated ions
J. Chem. Phys. 134 (2011) 144103, DOI: 10.1063/1.3567020, incl. supp. mat.

11.11
M. Reif, P.H. Hünenberger
Computation of methodology-independent single-ion solvation properties from molecular simulations IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water
JJ. Chem. Phys. 134 (2011) 144104, DOI: 10.1063/1.3567022, incl. supp. mat.

11.12
D. Steiner, C. Oostenbrink, F. Diederich, M. Zürcher, W.F van Gunsteren
Calculation of Binding Free Energies of Inhibitors to Plasmepsin II
J. Comput. Chem. 32 (2011) 1801-1812, DOI: 10.1002/jcc.21761, incl. supp. mat.

11.13
S. Riniker, A. P. E. Kunz, W. F. van Gunsteren
On the calculation of the dielectric permittivity of molecular models in the liquid phase
J. Chem. Theory Comput. 7 (2011) 1469-1475, DOI: org/10.1021/ct100610v

11.14
W. Huang, Z. Lin, W. F. van Gunsteren
Validation of the GROMOS 54A7 force field with respect to beta-peptide folding
J. Chem. Theory Comput. 7 (2011) 1237-1243, DOI: org/10.1021/ct100747y

11.15
Z. Lin, W. F. van Gunsteren, H. Liu
Conformational state-specific free energy differences by one-step perturbation: protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields
J. Comput. Chem. 32 (2011) 2290-2297, DOI: 10.1002/jcc.21818, incl. supp. mat

11.16
B. A. C. Horta, P. H. Hünenberger
Enantiomeric segregation in the gel phase of lipid bilayers
J. Am. Chem. Soc. 133 (2011) 8464-8466, DOI: dx.doi.org/10.1021/ja202479u

11.17
P. Limacher, H. P. Lüthi
Cross-conjugation
J.W. & S. Ltd. 1 (2011) 477-486, DOI: 10.1002/wcms.16

11.18
H. Satoh, S. Manabe, Y. Ito, H. P. Lüthi, T. Laino, J. Hutter
Endocyclic cleavage in glycosides with 2,3-trans cyclic protecting groups
J. Am. Chem. Soc.133 (2011) 5610-5619, DOI: dx.doi.org/10.1021/ja201024a

11.19
N. Schmid, A. P. Eichenberger, A. Choutko, S. Riniker, M. Winger, A. E. Mark, W. F. van Gunsteren
Definition and testing of the GROMOS force-field versions: 54A7 and 54B7
Eur. Biophys. J. 40 (2011), 843-856, DOI: 10.1007/s00249-011-0700-9, incl. supp. mat

11.20
S. Riniker, C.D. Christ, N. Hansen, A.E. Mark, P.C. Nair, W. F. van Gunsteren
Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors
J. Chem. Phys. 135 (2011), 024105, DOI: 10.1063/1.3604534, incl. supp. mat.

11.21
A. Kuzmanic, D. Kruschel, W. F. van Gunsteren, B. Zagrovic
Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures
J. Mol. Biol. 411 (2011), 286-297, DOI: 10.1016/j.jmb.2011.05.033, incl. supp. mat.

11.22
N. Schmid
Development and application of efficient, object-oriented software for simulation and structure refinement of biomolecules
Thesis Nr. 19630, ETH Zürich, 2011

11.23
A.P. Kunz, H. Liu, W. F. van Gunsteren
Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling
J. Chem. Phys. 135 (2011), 104106, DOI:10.1063/1.3629450, incl. supp. mat.

11.24
J. Dolenc, S. Riniker, R. Gaspari, X. Daura, W. F. van Gunsteren
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities
J. Comp. - Aided Mol. Des. 25 (2011), 709-716, DOI: 10.1007/s10822-011-9453-x

11.25
N. Schmid, J. Allison, J. Dolenc, A. P. Eichenberger, A. P. Kunz, W. F. van Gunsteren
Biomolecular structure refinement using the GROMOS simulation software
J. Biomolecular NMR. 51 (2011), 265-281, DOI: 10.1007/s10858-011-9534-0

11.26
A. P. Kunz, W. F. van Gunsteren
A method for conformational sampling of loops in protein based on adiabatic decoupling and temperature or force scaling
ChemPhysChem 12 (2011), 2609-2614, DOI: 10.1002/cphc. 201100305

11.27
A. P. Eichenberger, J. R. Allison, J. Dolenc, D. P. Geerke, B. A .C. Horta, K. Meier, C. Oostenbrink, N. Schmid, D. Steiner, D. Wang, W. F. van Gunsteren
The GROMOS++ software for the analysis of biomolecular simulation trajectories
J. Chem. Theory. Comp 7 (2011), 3379-3390, DOI: 10.1021/ct2003622

11.28
Z. Lin, W.F. van Gunsteren
Exploring the effect of side-chain substitutions upon the secondary structure preferences of beta-peptides
J. Phys. Chem. B 115 (2011) 12984-12992, DOI: 10.1021/jp2053508

11.29
N. Hansen, P. Kraus, H. Sassmannshausen, T. Timmerscheidt, W. F. van Gunsteren
An effective force field for molecular dynamics simulations of dimethyl sulfone
Mol. Phys. 109 (2011) 2593-2605, DOI: 10.1080/00268976.2011.624128

11.30
S. Riniker, C.D. Christ, N. Hansen, P. H. Hünenberger, C. Oostenbrink, D. Steiner, W. F. van Gunsteren
Calculation of relative free energies for ligand-protein binding, solvation and conformational transitions using the GROMOS software
J. Phys. Chem. B 115 (2011) 13570-13577, DOI: 10.1021/jp204303a

11.31
A. Choutko, W. F. van Gunsteren, P. H. Hünenberger
Preferential affinity of the components of liquid mixtures at a rigid non-polar surface:
Enthalpic and entropic driving forces
ChemPhysChem 12 (2011) 3214-3223, DOI: 10.1002/cphc201100541

11.32
Z. Lin, H. Liu, S. Riniker, W. F. van Gunsteren
On the use of enveloping distribution sampling (EDS) to compute free enthalpy differences between different conformational states of molecules: application to 3₁₀-, α, and л helices
J. Chem. Phys. 7 (2011) 3884-3897, DOI: 10.1021/ct200623b, incl. supp. mat.

2012

12.01
D. A. Niggli, M. O. Ebert, Z. Lin, D. Seebach, W. F. van Gunsteren
Helical content of a beta³-octapeptide in methanol: Molecular dynamics simulations explain a seeming discrepancy between conclusions derived from CD and NMR data
Chem. Eur. J. 18 (2012), 586-593, incl. supp. mat., DOI: 10.1002/chem.201102667

12.02
A. P. Eichenberger, L.J. Smith, W. F. van Gunsteren
Ester-linked hen egg white lysozyme shows a compact fold in a molecular dynamics simulation:
possible causes and sensitivity of experimentally observable quantities to structural changes maintaining this compact fold
FEBS 279 (2012), 299-315, DOI: 10.1111/j.1742-4658.2011.08424.x, incl. supp. mat.

12.03
K. Meier, W. Thiel, W. F. van Gunsteren
On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations
J. Comput. Chem. 33 (2012), 363-378, DOI: 10.1002/jcc.21962

12.04
A. P. E. Kunz, J. R. Allison, D. P. Geerke, B. A. C. Horta, P. H. Hünenberger, S. Riniker, N. Schmid, W. F. van Gunsteren
New functionalities in the GROMOS biomolecular simulation software
J. Comput. Chem. 33 (2012), 340-353, DOI: 10.1002/jcc.21954

12.05
N. Schmid, C.D. Christ, M.Christen, A.P. Eichenberger, W.F. van Gunsteren
Architecture, implementation and parallelization of the GROMOS software for biomolecular simulation
Comp. Phys. Comm. 183 (2012), 890-903, DOI: 10.1016/j.cpc.2011.12.014

in press

A.512
D. P. Geerke, F. Schwab and W. F. van Gunsteren
An Approach to Calculate the Free Energy of Dissolution of Salt Crystals from Molecular-Dynamics Simulations and its Application to Mixing of Lennard-Jones Liquids
xxxxx (2008) pending

A.572
T. S. Hofer, W.F. van Gunsteren
Exploring the properties of small molecule binding via molecular simulation: the TRSH – p53 core domain complex
xxxxx (2010) pending

A.610
J. Kleinjung, W. R. P. Scott, J. R. Allison, W. F. van Gunsteren, F. Fraternali
Implicit solvation parameters derived from explicit water forces in large-scale molecular dynamics simulations
J. Chem. Theory. Comp (2011) submitted, incl. supp. mat.

A.611
A. P. E. Kunz, Z. Lin, W. F. van Gunsteren
A method for sampling the internal degrees of freedom of a flexible solute molecule based on adiabatic decoupling and temperature or force scaling
Mol. Phys. (2011) accepted

A.612
J. R. Allison, M. Bergeler, W. F. van Gunsteren
Can computer modeling explain why two highly similar sequences fold into different structures?
Biochemistry (2011) online, incl. supp. mat., DOI: 10.1021/bi2015663

A.616
D. Steiner, W. F. van Gunsteren
An improved structural characterisation of reduced french bean plastocyanin
based on NMR data and local-elevation molecular dynamics simulation
J. Biomolecular NMR (2011) submitted, incl. supp. mat.

A.619
J. R. Allison, S. Riniker, W. F. van Gunsteren
Coarse-grained models for the solvents dimethyl sulfoxide, chloroform and methanol
J. Chem. Phys. (2011) accepted, incl. supp. mat.

A.621
N. Hansen, J. Dolenc, M. Knecht, S. Riniker, W.F. van Gunsteren
Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution
J. Comput. Chem. (2011) accepted, incl. supp. mat.

A.622
S. Riniker, B.A.C. Horta, B. Thijssen, S. Gupta, W.F. van Gunsteren, P.H. Hünenberger
Temperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: A molecular dynamics simulation study
ChemPhysChem (2011) accepted

A.623
B.A.C. Horta, Z. Lin, W. Huang, S. Riniker, W.F. van Gunsteren, P.H. Hünenberger
Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: influence on the folding properties of two beta-peptides in methanol
J. Comput. Chem. (2011) submitted

A.624
D. Wang, W.F. van Gunsteren, Z. Chai
Recent advances in computational actinide chemistry
Chem. Soc. Rev. (2012) submitted

A.625
D. Steiner, C. Oostenbrink, W.F. Van Gunsteren
Calculation of the Relative Free Energy of Oxidation of Azurin at pH 5 and pH 9
J. Comput. Chem. (2012) submitted, incl. supp. mat.