Paper Citing NAMD - Abstract
Penev, Evgeni S.; Lampoudi, Sotiria; Shea, Joan-Emma
TiREX: Replica-exchange molecular dynamics using TINKER
COMPUTER PHYSICS COMMUNICATIONS, 180:2013-2019, OCT 2009
We present a driver program for performing replica-exchange molecular dynamics simulations with the TINKER package. Parallelization is based on the Message Passing Interface, with every replica assigned to a separate process. The algorithm is not communication intensive, which makes the program suitable for running even on loosely Coupled cluster systems. Particular attention is paid to the practical aspects of analyzing the program Output. Program summary Program title: TiReX Catalogue identifier: AEEK_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEK_v1-0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qLib.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 43 385 No. of bytes in distributed program, including test data, etc.: 502 262 Distribution format: tar.gz Programming language: Fortran 90/95 Computer: Most UNIX machines Operating system: Linux Has the code been vectorized or parallelized?: parallelized with MPI Classification: 16.13 External routines: TINKER version 4.2 or 5.0, built as a library Nature of problem: Replica-exchange molecular dynamics. Solution method: Each replica is assigned to a separate process; temperatures are swapped between replicas at regular time intervals. Running time: The sample run may take up to a few minutes. (C) 2009 Elsevier B.V. All rights reserved.
