A general purpose parallel molecular dynamics simulation program

KJ Oh and ML Klein, COMPUTER PHYSICS COMMUNICATIONS, 174, 560-568 (2006).

DOI: 10.1016/j.cpc.2005.12.002

We present a general purpose parallel molecular dynamics simulation code. The code can handle NVE, NVT, and NPT ensemble molecular dynamics, Langevin dynamics, and dissipative particle dynamics. Long-range interactions are handled by using the smooth particle mesh Ewald method. The implicit solvent model using solvent-accessible surface area was also implemented. Benchmark results using molecular dynamics, Langevin dynamics, and dissipative particle dynamics are given. Program summary Title of program: MM-PAR Catalogue identifier: ADXP-v 1 -0 Program summary URL: http://cpc.cs.qub.ac.uk/suminaries/ADXP - v I - 0 Program obtainable from: CPC Program Library. Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: any UNIX machine. The code has been tested on Linux cluster and IBM p690 Operating systems or monitors under which the program has been tested: Linux, AIX Programming language used: C Memory required to execute with typical data: similar to 60 MB for a system of similar to 24 000 atoms Has the code been vectorized or parallelized? parallelized with MPI using atom decomposition and domain decomposition No. of lines in distributed program, including test data, etc.: 171427 No. of bytes in distributed program, including test data, etc.: 4 558 773 Distribution format: tar.gz External routines/libraries used: FFTW free software (http://www.fftw.org) Nature of physical problem: Structural, thermodynamic, and dynamical properties of fluids and solids from microscopic scales to mesoscopic scales. Method of solution: Molecular dynamics simulation in NVE. NVT, and NPT ensemble, Langevin dynamics simulation, dissipative particle dynamics simulation. Typical running time: Table below shows the typical run times for the four test programs. GRAPHICS (C) 2005 Elsevier B.V. All rights reserved.

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