During recent decades it has become feasible to simulate the dynamics of molecular systems on a computer. The method of molecular dynamics (MD) solves Newton's equations of motion for a molecular system, which results in trajectories for all atoms in the system. From these atomic trajectories a variety of properties can be calculated. The aim of computer simulations of molecular systems is t o compute macroscopic behavior from microscopic interactions. The main contributions a microscopic consideration can offer are (1) the understanding and (2) interpretation of experimental results, (3) semiquantitative estimates of experimental results, and (4) the capability to interpolate or extrapolate experimental data into regions that are only difficultly accessible in the laboratory. One of the two basic problems in the field of molecular modeling and simulation is how to efficiently search the vast configuration space which is spanned by all possible molecular conformations for the global low (free) energy regions which will be populated by a molecular system in thermal equilibrium. The other basic problem is the derivation of a sufficiently accurate interaction energy function or force field for the molecular system of interest. An important part of the art of computer simulation is to choose the unavoidable assumptions, approximations and simplifications of the molecular model and computational procedure such that their contributions to the overall inaccuracy are of comparable size, without affecting significantly the property of interest. Methodology and some practical applications of computer simulation in the field of (bio)chemistry will be reviewed.

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Phosphate moieties bind frequently at N-termini of helices in proteins. It is shown that this corresponds with an optimal interaction of the helix dipole and the charged phosphate. This favourable arrangement may have been discovered several times during evolution. In some enzymes, the helix dipole might be used in catalysis.

SynopsisA simple point-charge potential, developed earlier for the calculation of intermolecular forces in molecular-dynamics simulations of liquid water, has been extended to include interactions between water molecules and polar groups of proteins. A complete potential for use in the simulation of protein dynamics in water is reported.

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