Implementation of accelerated molecular dynamics in NAMD

Y. Wang, C. B. Harrison, K. Schulten, J. A. McCammon

Research output: Contribution to journalArticlepeer-review

Abstract

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 interpretation of aMD results, as well as the advantages and limitations of the aMD method.

Original languageEnglish (US)
Article number015002
JournalComputational Science and Discovery
Volume4
Issue number1
DOIs
StatePublished - Dec 2011

ASJC Scopus subject areas

  • Numerical Analysis
  • Physics and Astronomy(all)
  • Computational Mathematics

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