Implementation of Accelerated Molecular Dynamics in NAMD.
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ABSTRACT:
SUBMITTER: Wang Y
PROVIDER: S-EPMC3115733 | biostudies-literature | 2011
REPOSITORIES: biostudies-literature
Publications
Implementation of Accelerated Molecular Dynamics in NAMD.
Wang Yi Y Harrison Christopher B CB Schulten Klaus K McCammon J Andrew JA
Computational science & discovery 20110101 1
Accelerated molecular dynamics (aMD) is an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. Here we present the implementation of aMD in the parallel simulation program NAMD. We show that aMD simulations performed with NAMD have only a small overhead compared with classical MD simulations. Through example applications to the alanine dipeptide, we discuss the choice of acceleration parameters, the interpr ...[more]
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