Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange.

ABSTRACT: Today's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of degrees of freedom involved. Aiming at increased sampling efficiency, we present a novel simulation method combining the ideas of essential dynamics and REX. Unlike standard REX, in each replica only a selection of essential collective modes of a subsystem of interest (essential subspace) is coupled to a higher temperature, with the remainder of the system staying at a reference temperature, T(0). T

SUBMITTER: Kubitzki MB 

PROVIDER: S-EPMC1877756 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature