ISSN:
0192-8651
Keywords:
Computational Chemistry and Molecular Modeling
;
Biochemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
,
Computer Science
Notes:
A detailed description of vector/parallel algorithms for the molecular dynamics (MD) simulation of macromolecular systems on multiple processor, shared-memory computers is presented. The algorithms encompass three computationally intensive portions of typical MD programs: (1) the evaluation of the potential energies and forces, (2) the generation of the nonbonded neighbor list, and (3) the satisfaction of holonomic constraints. We implemented the algorithms into two standard programs; CHARMM and AMBER, and obtained near linear speedups on eight processors of a Cray Y-MP for cases (1) and (2). For case (3) the SHAKE method demonstrated a speedup of 6.0 on eight processors while the matrix inversion method demonstrated 6.4. For a system of water molecules the performance improvement over the standard scalar SHAKE subroutine in AMBER ranged from a factor of 165 to greater than 2000.
Additional Material:
5 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/jcc.540121016
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