Efficiency in statistical mechanical simulations of biomolecules — computer programs for molecular and continuum modelling

Abstract

A strategy for biomolecular simulations is described. It includes a molecular dynamics (MD) simulation program and a Monte Carlo (MC) simulation program. The former provides a molecular description including a classical treatment of covalent bonds and bond angles. The MD program has been carefully tuned for optimal efficiency, while remaining completely general and capable of handling all kinds of mixtures of flexible molecules. It also allows one to incorporate 2D NMR constraints for structural refinement. The MC program is designed for studies of long-range electrostatic interactions - the basic system is an arbitrarily shaped charged aggregate solvated in a salt solution. The approach is based on a dielectric continuum model and only electrostatic interactions are treated explicitly. The solvent enters as a dielectric medium screening the electrostatic interactions with a appropriate dielectric permittivity.