Paper Citing NAMD - Abstract
Brown, Aaron H.; Walsh, Tiffany R.
An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture
COMPUTER PHYSICS COMMUNICATIONS, 192:278-281, JUL 2015
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 simulations. Our implementation is compatible with a range of architectures; crucially it enables the use of this wrapper with the BlueGene/Q architecture, in addition to the x86 architecture. Program summary Program title: TIGER2-NAMD Catalogue identifier: AEWC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard-CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 34151 No. of bytes in distributed program, including test data, etc.: 424217 Distribution format: tar.gz Programming language: Tcl 8.5. Computer: x86 Clusters, BlueGene/Q Workstations. Operating system: Linux, IBM Compute Node Kernel. Has the code been vectorised or parallelised?: Yes. MPI Parallelism. Classification: 3. External routines: NAMD 2.9 (http://www.ks.uiuc.edu/Research/namd/) Nature of problem: Replica Exchange Molecular Dynamics Solution method: Each replica runs through multiple cycles of heating and cooling with exchanges between them being attempted. Running time: Typically 30 mins, up to an hour (C) 2015 Elsevier B.V. All rights reserved.
