T. Huber et Wf. Vangunsteren, SWARM-MD - SEARCHING CONFORMATIONAL SPACE BY COOPERATIVE MOLECULAR-DYNAMICS, The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 102(29), 1998, pp. 5937-5943
A simulation algorithm is introduced, which uses a swarm of molecules
to explore conformational space. The method uses multiple, different s
tarting conformations and propagates them in time by integration of Ne
wton's equation of motion. In contrast to conventional molecular dynam
ics simulation of a set of independent molecules, in this method each
molecule of the swarm is in addition subject to an artificial field th
at keeps the trajectory of individual molecules tied to the average tr
ajectory 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 min
ima in the potential energy surface and that the total system is more
likely to follow an overall potential energy gradient toward the globa
l energy minima.