Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions.

ABSTRACT: We introduce an enhanced-sampling method for molecular dynamics (MD) simulations referred to as ensemble-biased metadynamics (EBMetaD). The method biases a conventional MD simulation to sample a molecular ensemble that is consistent with one or more probability distributions known a priori, e.g., experimental intramolecular distance distributions obtained by double electron-electron resonance or other spectroscopic techniques. To this end, EBMetaD adds an adaptive biasing potential throughout the simulation that discourages sampling of configurations inconsistent with the target probability distributions. The bias introduced is the minimum necessary to fulfill the target distributions, i.e., EBMetaD satisfies the maximum-entropy principle. Unlike other methods, EBMetaD does not require mul

SUBMITTER: Marinelli F 

PROVIDER: S-EPMC4472218 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature