Dynamics in Rugged Energy Landscapes with Applications to the S-Peptide and Ribonuclease A

A simple means of computing the rate of conformational space sampling and energy transfer in computer simulations of biomolecules using replica molecular dynamics is described. The method is based on the idea that in an ergodic system trajectories should be self-averaging-properties measured over two independent trajectories must average to the same result. Replica molecular dynamics simulation is used to calculate the generalized ergodic measure and the rate of self-averaging for the force and potential energy for the S-peptide and RNase A enzyme over a range of temperatures from 40 to 400 K