Coupling of replica exchange simulations to a non-Boltzmann structure reservoir.

ABSTRACT: Computing converged ensemble properties remains challenging for large biomolecules. Replica exchange molecular dynamics (REMD) can significantly increase the efficiency of conformational sampling by using high temperatures to escape kinetic traps. Several groups, including ours, introduced the idea of coupling replica exchange to a pre-converged, Boltzmann-populated reservoir, usually at a temperature higher than that of the highest temperature replica. This procedure reduces computational cost because the long simulation times needed for extensive sampling are only carried out for a single temperature. However, a weakness of the approach is that the Boltzmann-weighted reservoir can still be difficult to generate. We now present the idea of employing a non-Boltzmann reservoir, whose struct

SUBMITTER: Roitberg AE 

PROVIDER: S-EPMC4819981 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature