A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations

Published: 1 January 2015| Version 1 | DOI: 10.17632/yk73j46v4b.1
Sunhwan Jo, Wei Jiang


Abstract Replica Exchange with Solute Tempering (REST2) is a powerful sampling enhancement algorithm of molecular dynamics (MD) in that it needs significantly smaller number of replicas but achieves higher sampling efficiency relative to standard temperature exchange algorithm. In this paper, we extend the applicability of REST2 for quantitative biophysical simulations through a robust and generic implementation in greatly scalable MD software NAMD. The rescaling procedure of force field parameters co... Title of program: REST2-NAMD Catalogue Id: AEXX_v1_0 Nature of problem A generic implementation providing user-friendly API including input file preparation and performing replica exchange, and high frequency exchange attempt frequency with minimal communication overhead. Versions of this program held in the CPC repository in Mendeley Data AEXX_v1_0; REST2-NAMD; 10.1016/j.cpc.2015.08.030 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)



Molecular Biology, Biological Sciences, Computational Physics