Replica exchange with dynamical scaling.
A replica exchange method is presented which requires fewer replicas and is designed to be used for large systems. In this method, dynamically scaled replicas are placed between conventional replicas at broadly spaced temperatures. The potential of the scaled replicas is linearly scaled by a dynamical variable which varies between 0 and 1. When the variable is near either end point the replica can undergo exchanges with one of its neighboring replicas. Two different versions of the method are presented for a model system of a small peptide in water. The scaled replica can replace many replicas and the method can be up to ten times more efficient than conventional replica exchange.
Rick
Steven W
SW
Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA. srick@uno.edu
D000465:Algorithms; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry; D008954:Models, Biological; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D055672:Static Electricity; D013696:Temperature; D013997:Time Factors; D014867:Water / Q000737:chemistry*
D004151:Dipeptides; D010455:Peptides; D014867:Water; C002956:alanylalanine