Implementation of accelerated molecular dynamics in NAMD

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 per...

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Bibliographic Details
Published inComputational science & discovery Vol. 4; no. 1; pp. 015002 - 1-10
Main Authors Wang, Y, Harrison, C B, Schulten, K, McCammon, J A
Format Journal Article
LanguageEnglish
Published England IOP Publishing 01.01.2011
Subjects
Alanine
Barriers
Computation
Computer simulation
Dynamical systems
Dynamics
Molecular dynamics
Sampling
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Summary: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.
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ISSN:1749-4699
1749-4680
1749-4699
DOI:10.1088/1749-4699/4/1/015002