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TNAMD: Implementation of TIGER2 in NAMD

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dc.contributor.authorMenz, W.
dc.contributor.authorPenna, M.
dc.contributor.authorBiggs, M.
dc.date.issued2010
dc.description.abstractReplica-exchange molecular dynamics (REMD) must be used to enhance sampling when there are significant (relative to kT) barriers between different parts of the phase space. TIGER2 is a next-generation REMD method that offers more efficient sampling compared to the original REMD method by reducing the number of replicas required to span a given temperature range. In this paper, we present an implementation of the TIGER2 algorithm in the NAMD software package. This implementation exploits the capacity of NAMD to interpret Tcl scripts. The Tcl script implementing TIGER2 is provided and explained in detail, and demonstrated for alanine dipeptide in water. © 2010 Elsevier B.V. All rights reserved.
dc.description.statementofresponsibilityWilliam J. Menz, Matthew J. Penna, Mark J. Biggs
dc.identifier.citationComputer Physics Communications, 2010; 181(12):2082-2085
dc.identifier.doi10.1016/j.cpc.2010.09.011
dc.identifier.issn0010-4655
dc.identifier.issn1879-2944
dc.identifier.urihttp://hdl.handle.net/2440/63253
dc.language.isoen
dc.publisherElsevier Science BV
dc.rightsCopyright © 2010 Elsevier B.V. All rights reserved.
dc.source.urihttps://doi.org/10.1016/j.cpc.2010.09.011
dc.subjectMolecular dynamics
dc.subjectReplica-exchange molecular dynamics
dc.subjectNAMD
dc.subjectTIGER2 method
dc.subjectTool command language
dc.subjectFree energy prediction
dc.titleTNAMD: Implementation of TIGER2 in NAMD
dc.typeJournal article
pubs.publication-statusPublished

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