Free-energy calculation via mean-force dynamics using a logarithmic energy landscape

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jun;85(6 Pt 2):066702. doi: 10.1103/PhysRevE.85.066702. Epub 2012 Jun 11.

Abstract

A method for free-energy calculation based on mean-force dynamics (fictitious dynamics on a potential of mean force) is presented. The method utilizes a logarithmic form of free energy to enhance crossing barriers on a free-energy landscape, which results in efficient sampling of "rare" events. Invoking a conserved quantity in mean-force dynamics, free energy can be estimated on-the-fly without postprocessing. This means that an estimate of the free-energy profile can be locally made in contrast to the other methods based on mean-force dynamics such as metadynamics. The method is benchmarked against conventional methods and its high efficiency is demonstrated in the free-energy calculation for a glycine dipeptide molecule.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computer Simulation
  • Energy Transfer*
  • Entropy*
  • Models, Theoretical*
  • Stress, Mechanical