Some recent techniques for free energy calculations

Research output: Contribution to journalArticlepeer-review

Abstract

A few recent techniques to calculate free energies in the context of molecular dynamics simulations are discussed: temperature-accelerated molecular dynamics, which is a method, to explore fast the important regions in the free energy landscape associated with a set of continuous collective variables without having to know where these regions are beforehand; the single sweep method, which is a variational method to interpolate the free energy globally given a set of mean forces (i.e., a set of gradients of the free energy) calculated at specific points, or centers, on the free energy landscape; and a Voronoi-based free energy method, for the calculation of the free energy of the Voronoi tessellation associated with a set of centers. We also discuss how this last technique can be used, in conjunction with the string method, and how kinetic information such as reaction rates can be calculated by milestoning using the edges of a Voronoi tessellation as milestones.

Original languageEnglish (US)
Pages (from-to)1737-1747
Number of pages11
JournalJournal of Computational Chemistry
Volume30
Issue number11
DOIs
StatePublished - Aug 2009

Keywords

  • Free energy
  • Markov state model
  • Milestoning
  • Single sweep
  • String method
  • Temperature accelerated
  • Voronoi tessellation

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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