SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics

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.