A parallel molecular dynamics simulation scheme for a molecular system with bond constraints in NPT ensemble

KJ Oh and ML Klein, COMPUTER PHYSICS COMMUNICATIONS, 174, 263-269 (2006).

DOI: 10.1016/j.cpc.2005.10.011

Equations of motion based on an atomic group scaling scheme are described for a molecular system with bond constraints. The NPT ensemble extended system method is employed along with a numerical integration scheme using an operator technique. For parallelization of the integration scheme, a domain decomposition scheme is employed based on a group of atoms which share common constraints. This decomposition scheme fits well into the integration scheme and involves no extra inter- processor communication during the SHAKE/RATTLE procedures. An example is given for a solvated protein system containing a total of 23 558 atoms on 64 processors. (c) 2005 Elsevier B.V. All rights reserved.

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