An optimized replica exchange molecular dynamics method

J Chem Phys. 2009 Feb 21;130(7):074906. doi: 10.1063/1.3077857.

Abstract

We introduce a new way to perform swaps between replicas in replica exchange molecular dynamics simulations. The method is based on a generalized canonical probability distribution function and flattens the potential of mean force along the temperature coordinate, such that a random walk in temperature space is achieved. Application to a Go model of protein A showed that the method is more efficient than conventional replica exchange. The method results in a constant probability distribution of the replicas over the thermostats, yields a minimum round-trip time between extremum temperatures, and leads to faster ergodic convergence.

Publication types

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

MeSH terms

  • Algorithms
  • Hot Temperature
  • Models, Molecular*
  • Probability
  • Protein Denaturation
  • Protein Folding
  • Protein Structure, Secondary
  • Staphylococcal Protein A / chemistry
  • Thermodynamics

Substances

  • Staphylococcal Protein A