The reliability of the molecular models, force fields and computational procedures can be established by a comparison of simulated properties with known experimental ones, for various types of molecules: water, chloroform, DMSO, peptides, proteins, DNA, carbohydrates. The introduction of polarisability in the force field for biomolecules is investigated. Methods for the proper treatment of long-range electrostatic interactions are being developed.
The quality of the interaction function or force field that describes the forces between the atoms of a biomolecular system is of decisive importance for the predictive power of MD simulations. Therefore, we have over the past decade spent much effort to gradually improve the GROMOS force field whenever results of simulation applications pointed at force field deficiencies. The first set of (non-bonded) GROMOS force field parameters dates from 1984 [84.01]. Since then, the force field has continuously been improved and refined [95.23, 98.02, 00.22, 01.26, 03.04, 04.28, 05.07, 05.27, 09.11, 09.24, 11.05, 11.08, 11.19]. The most widely used versions of the GROMOS force field are the GROMOS 37C4 force field of 1985, the GROMOS 43A1 force field of 1996 [96.40, 98.02] and the GROMOS 45A3 force field of 2001 [01.26]. The currently used versions are the 45A4 parameter set [03.04, 05.07, 05.27], the 53A5/6 [04.28], and the 54A7 one [09.24, 11.19, 13.24]. In parallel to the development of force field parameters for biomolecules, solvent models that are consistent with the GROMOS biomolecular force field were developed for much used (co-)solvents [06.06]: water [81.04, 02.18], methanol [00.09], DMSO [04.06], chloroform [94.36], carbontetrachloride [96.33], urea [04.05], acetonitrile [06.02], dimethyl sulfone [11.29]. Polarisable (solvent) models are available for water [14.14], methanol [06.22], DMSO [14.07], chloroform [10.20], carbotetrachloride [11.02], urea [15.05], acetone [A104], n-alkanes [14.04]. Supra molecular polarisable coarse-grained solvent models are available for water [11.03], methanol [12.07, 14.05], DMSO [12.07], chloroform [12.07], and for n-alkanes [15.14] and cyclohexane [15.07].
Major Algorithmic Contributions
- Force-field parametrisation using the weak-coupling technique [95.14]
- Force-field parameterisation using quasi-Newtonian dynamics for the parameters [97.05]