An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture

Published: 1 January 2015| Version 1 | DOI: 10.17632/5s8dnj8fz2.1
Aaron H. Brown, Tiffany R. Walsh


Abstract Here we present an improved implementation of the TIGER2 Replica Exchange Molecular Dynamics (REMD) method, using the replica exchange Application Programming Interface (API) found in contemporary versions of the NAMD Molecular Dynamics Package. The implementation takes the form of a TCL script which is used in conjunction with the standard configuration file. This implementation is validated against a previous TIGER2 implementation, as well as data reported for the original TIGER2 simulation... Title of program: TIGER2-NAMD Catalogue Id: AEWC_v1_0 Nature of problem Replica Exchange Molecular Dynamics Versions of this program held in the CPC repository in Mendeley Data AEWC_v1_0; TIGER2-NAMD; 10.1016/j.cpc.2015.02.025 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)



Molecular Biology, Biological Sciences, Computational Physics