TNAMD: Implementation of TIGER2 in NAMD

William J. Menz, Matthew J. Penna, Mark J. Biggs

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Replica-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.

Original languageEnglish
Pages (from-to)2082-2085
Number of pages4
JournalComputer Physics Communications
Volume181
Issue number12
DOIs
Publication statusPublished - Dec 2010

Keywords

  • Free energy prediction
  • Molecular dynamics
  • NAMD
  • Replica-exchange molecular dynamics
  • TIGER2 method
  • Tool command language

ASJC Scopus subject areas

  • Hardware and Architecture
  • Physics and Astronomy(all)

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