Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm

Abstract

This chapter discusses the atomic simulations of protein folding, using the replica exchange (RE) algorithm. In REs method, several copies or replicas of a system are simulated in parallel, only occasionally exchanging temperatures through a Monte Carlo (MC) move that maintains detailed balance. This algorithm is ideal for a large cluster of poorly communicating processors because temperature exchanges can be relatively infrequent and require little data transfer. It was adapted for use with molecular dynamics and named the replica exchange molecular dynamics (REMD) method. The essence of the REMD method is to use the molecular dynamics to generate a suitable canonical ensemble in each replica rather than MC. REMD normally occurs in coordinate and momentum space instead of just coordinate space. The typical temperature fluctuations and their relation to conformational changes are demonstrated from an actual REMD simulation of a solvated peptide. The use of REMD to study the thermodynamics of helix-coil transitions in peptides that are experimentally characterized is also elaborated.