Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics

J Chem Theory Comput. 2015 Nov 10;11(11):5062-7. doi: 10.1021/acs.jctc.5b00846. Epub 2015 Oct 9.

Abstract

Metadynamics accelerates sampling of molecular dynamics while reconstructing thermodynamic properties of selected descriptors of the system. Its main practical difficulty originates from the compromise between keeping the number of descriptors small for efficiently exploring their multidimensional free-energy landscape and biasing all of the slow motions of a process. Here we illustrate on a model system and on the tryptophan-cage miniprotein parallel bias metadynamics, a method that overcomes this issue by simultaneously applying multiple low-dimensional bias potentials.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Models, Biological
  • Molecular Dynamics Simulation*
  • Thermodynamics*
  • Tryptophan / chemistry*

Substances

  • Tryptophan