Paper Info
Title
A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations.
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 controlling REST2 “hot region” is implemented into NAMD at the source code level. A user can conveniently select hot region through VMD and write the selection information into a PDB file. The rescaling keyword/parameter is written in NAMD Tcl script interface that enables an on-the-fly simulation parameter change. Our implementation of REST2 is within communication-enabled Tcl script built on top of Charm++, thus communication overhead of an exchange attempt is vanishingly small. Such a generic implementation facilitates seamless cooperation between REST2 and other modules of NAMD to provide enhanced sampling for complex biomolecular simulations. Three challenging applications including native REST2 simulation for peptide folding–unfolding transition, free energy perturbation/REST2 for absolute binding affinity of protein–ligand complex and umbrella sampling/REST2 Hamiltonian exchange for free energy landscape calculation were carried out on IBM Blue Gene/Q supercomputer to demonstrate efficacy of REST2 based on the present implementation.
Year
DOI
Venue
2015
10.1016/j.cpc.2015.08.030
Computer Physics Communications
Keywords
Field
DocType
REST2,NAMD,Tcl,Free energy calculation
System software,Byte,Replica,Supercomputer,Source code,Computer science,Parallel computing,Algorithm,Software,Test data,Scalability
Journal
Volume
ISSN
Citations 
197
0010-4655
0
PageRank 
References 
Authors
0.34
7
2
Name
Order
Citations
PageRank
Sunhwan Jo113413.08
Wei Jiang2131.94