Molecular Dynamics The Entropy Problem

In principle, classical molecular dynamics involves motion on the potential energy surface (PES). We assume that the temperature is sufficiently high to avoid problems with motion involving the lowest vibrational levels, where quantiun mechanics tends to complicate the problem. We also assume that the motion takes place on the ground state energy surface. There is no surface-crossing problem of the type that we discussed in Section 4.7. 

The enthalpy change AH is included in the PES, obtained, for example, from the SE. In molecular dynamics, we solve the Newton equations for the great number of particles with PES as potential function. 

on the other hand, AH is positive, solvation may proceed anyway, since the increase in S may be so large that AG 0. In this case, there will be a slowing down of the particles. The problem is to calculate this slowing down in molecular dynamics. 

To have a macrosystem to compare with, we may imagine a male rolling skater. If he skates down the hill, his speed will, of course, increase at the bottom of the 

A molecnlar dynamics problem of this sort is simulation of ligand escape. For example, one may be interested in calculating the rate of O2 escaping into hemoglobin, the oxygen carrier in blood. Unfortunately, we cannot discuss this problem here. 

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