Dr. Anatoly Malevanets
Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario, Canada
Multiple Replica Repulsion Technique for Efficient Conformational Sampling of
Biological Systems
Abstract
A new technique for sampling complex molecular systems with
many degrees of freedom is proposed. 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 a
portion 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.