Gaussian-Mixture Umbrella Sampling
Publication information:
Maragakis P, Vaart A, Karplus M. Gaussian-Mixture Umbrella Sampling. J. Phys. Chem. B. 2009;113(14):4664–4673.
Abstract
We introduce the Gaussian-mixt. umbrella sampling method (GAMUS), a biased mol. dynamics technique based on adaptive umbrella sampling that efficiently escapes free energy min. in multidimensional problems. The prior simulation data are reweighted with a max. likelihood formulation, and the new approx. probability d. is fit to a Gaussian-mixt. model, augmented by information about the unsampled areas. The method can be used to identify free energy min. in multidimensional reaction coordinates. To illustrate GAMUS, we apply it to the alanine dipeptide (2D reaction coordinate) and tripeptide (4D reaction coordinate).