Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.

ABSTRACT: Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is

SUBMITTER: Roe DR 

PROVIDER: S-EPMC3983400 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature