Gaussian-mixture umbrella sampling

J Phys Chem B. 2009 Apr 9;113(14):4664-73. doi: 10.1021/jp808381s.

Abstract

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).

MeSH terms

  • Alanine / chemistry*
  • Computer Simulation
  • Models, Chemical
  • Oligopeptides / chemistry*

Substances

  • Oligopeptides
  • Alanine