TCB Publications - Abstract

Yi Wang, Chris B. Harrison, Klaus Schulten, and J. Andrew McCammon. Implementation of accelerated molecular dynamics in NAMD. Computational Science & Discovery, 4:015002, 2011. (PMC: PMC3115733)

WANG2011 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 also discuss the choice of acceleration parameters and the interpretation of aMD results.

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