Gaussian-mixture umbrella sampling.
We introduce the Gaussian-mixture umbrella sampling method (GAMUS) , a biased molecular dynamics technique based on adaptive umbrella sampling that efficiently escapes free energy minima in multidimensional problems. The prior simulation data are reweighted with a maximum likelihood formulation, and the new approximate probability density is fit to a Gaussian-mixture model, augmented by information about the unsampled areas. The method can be used to identify free energy minima in multidimensional reaction coordinates. To illustrate GAMUS , we apply it to the alanine dipeptide (2D reaction coordinate) and tripeptide (4D reaction coordinate).
Maragakis
Paul
P
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA. paul.maragakis@DEShawResearch.com
van der Vaart
Arjan
A
Karplus
Martin
M
D000409:Alanine / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D009842:Oligopeptides / Q000737:chemistry*
D009842:Oligopeptides; D000409:Alanine