A simple rigid three-site model for methanol compatible with the simple point charge ͑SPC͒ water and the GROMOS96 force field is parametrized and tested. The influence of different force-field parameters, such as the methanol geometry and the charge distribution on several properties calculated by molecular dynamics is investigated. In particular an attempt was made to obtain good agreement with experimental data for the static dielectric constant and the mixing enthalpy with water. The model is compared to other methanol models from the literature in terms of the ability to reproduce a range of experimental properties.

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Eight molecular dynamics simulations of a ubiquitin crystal unit cell were performed to investigate the effect of different schemes to treat the long-range electrostatic interactions as well as the need to include counter ions. A crystal system was chosen as the test system, because the higher charge density compared with a protein in solution makes it more sensitive to the way of treating the electrostatic interactions. Three different schemes of treating the long-range interactions were compared: straight cutoff, reaction-field approximation, and a lattice-sum method (P3M). For each of these schemes, two simulations were performed, one with and one without the counter ions. Two additional simulations with a reaction-field force and different initial placements of the counter ions were performed to examine the effect of the initial positions of the ions. The inclusion of long-range electrostatic interactions using either a reaction-field or a lattice-sum method proved to be necessary for the simulation of crystals. These two schemes did not differ much in their ability to reproduce the crystallographic structure. The inclusion of counter ions, on the other hand, seems not necessary for obtaining a stable simulation. The initial positions of the ions have a visible but small effect on the simulation.

In order to investigate the dependence of the viscosity on the mass of the molecules in a liquid, and thus check the validity of Stokes' law for molecules, several molecular dynamics simulations of 'water' molecules with different mass and different molecular mass distributions were performed. The viscosity is shown to be sensitive to the mass but less sensitive to the mass distribution. The product of diffusion coefficient and viscosity, which according to Stokes' law should be independent of the mass, varies. We may therefore conclude that Stokes' law is not valid for small molecules. q 1999 Elsevier Science B.V. All rights reserved.

Molecular dynamics simulations of protein folding and unfolding are often carried out at temperatures (400-600 K) that are much higher than physiological or room temperature to speed up the (un)folding process. Use of such high temperatures changes both the protein and solvent properties considerably, compared to physiological or room temperature. Water models designed for use in conjunction with biomolecules, such as the simple point charge (SPC) model, have generally been calibrated at room temperature and pressure. To determine the distortive effect of high simulation temperatures on the behavior of such "room temperature" water models, the structural, dynamic, and thermodynamic properties of the much-used SPC water model are investigated in the temperature range from 300 to 500 K. Both constant pressure and constant volume conditions, as used in protein simulations, were analyzed. We found that all properties analyzed change markedly with increasing temperature, but no phase transition in this temperature range was observed.