Calculating potentials of mean force from steered molecular dynamics simulations

Sanghyun Park, Klaus Schulten

Research output: Contribution to journalReview articlepeer-review

Abstract

The theoretical and practical issues concerned with the calculation of potential of mean forces from steered molecular dynamics (SMD) were discussed. The derivation of Jarzynski equality was reviewed, the equality was generalized to isobaric-isothermal processes, and its implications were discussed in relation to the second law of thermodynamics and computer simulations. The Gaussian nature of work distributions for an exemplary simulation was demonstrated. This result supports the use of the second order cumulant expansion in practical application of Jarzynski's equality in SMD simulations.

Original languageEnglish (US)
Pages (from-to)5946-5961
Number of pages16
JournalJournal of Chemical Physics
Volume120
Issue number13
DOIs
StatePublished - Apr 1 2004

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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