Multiple replica repulsion technique for efficient conformational sampling of biological systems.

ABSTRACT: Here, we propose a technique for sampling complex molecular systems with many degrees of freedom. The technique, termed "multiple replica repulsion" (MRR), does not suffer from poor scaling with the number of degrees of freedom associated with common replica exchange procedures and does not require sampling at high temperatures. The algorithm involves creation of multiple copies (replicas) of the system, which interact with one another through a repulsive potential that can be applied to the system as a whole or to portions of it. The proposed scheme prevents oversampling of the most populated states and provides accurate descriptions of conformational perturbations typically associated with sampling ground-state energy wells. The performance of MRR is illustrated for three systems of incr

SUBMITTER: Malevanets A 

PROVIDER: S-EPMC3175088 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature