TNAMD: Implementation of TIGER2 in NAMD

Published: 1 December 2010| Version 1 | DOI: 10.17632/2nmrgvdg5w.1
William J. Menz, Matthew J. Penna, Mark J. Biggs


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 c... Title of program: TNAMD Catalogue Id: AEHH_v1_0 Nature of problem Replica-exchange molecular dynamics Versions of this program held in the CPC repository in Mendeley Data AEHH_v1_0; TNAMD; 10.1016/j.cpc.2010.09.011 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)



Molecular Biology, Biological Sciences, Computational Physics