title: Implementation of Accelerated Molecular Dynamics in NAMD.
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.
authors.affiliation: Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, University of California, San Diego, La Jolla, 92093, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Harrison
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon