Comparison of free energy surfaces for extended-atom and all-atom models of n-butane

The dependence of conformational energy on the central torsion angle of butane (phi) has been examined for an all-atom and for an extended-atom model, using molecular dynamics (MD). Conformational space was sampled with a special umbrella sampling potential that optimizes sampling statistics. Although the shapes of the free energy surfaces of the two models are similar, there are substantial differences in the dependence of entropy on phi. Anharmonic effects make important contributions to the entropy in the extended-atom model. In the extended atom model, the dependence of internal energy on phi is quite different when determined by MD than when determined by energy minimization, suggesting that potential function parameters that have been refined by energy minimization may not always be suitable for MD simulations.