SWARM-MD: searching conformational space by cooperative molecular dynamics

Huber, Thomas and van Gunsteren, Wilfred F. (1998) SWARM-MD: searching conformational space by cooperative molecular dynamics. Journal of Physical Chemistry A, 102 29: 5937-5943. doi:10.1021/jp9806258

Author Huber, Thomas
van Gunsteren, Wilfred F.
Title SWARM-MD: searching conformational space by cooperative molecular dynamics
Journal name Journal of Physical Chemistry A   Check publisher's open access policy
ISSN 1089-5639
Publication date 1998-07-16
Sub-type Article (original research)
DOI 10.1021/jp9806258
Volume 102
Issue 29
Start page 5937
End page 5943
Total pages 7
Place of publication Washington, D.C. U.S.A.
Publisher American Chemical Society
Language eng
Subject 030402 Biomolecular Modelling and Design
030505 Physical Organic Chemistry
Abstract A simulation algorithm is introduced, which uses a swarm of molecules to explore conformational space. The method uses multiple, different starting conformations and propagates them in time by integration of Newton's equation of motion. In contrast to conventional molecular dynamics simulation of a set of independent molecules, in this method each molecule of the swarm is in addition subject to an artificial field that keeps the trajectory of individual molecules tied to the average trajectory of the swarm. In this manner, a search for the global energy minima of many molecules is transformed into a cooperative search. It is shown that such a cooperative search is less attracted by local minima in the potential energy surface and that the total system is more likely to follow an overall potential energy gradient toward the global energy minima.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
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