Microcanonical replica exchange molecular dynamics simulation of proteins

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Nov;80(5 Pt 2):056703. doi: 10.1103/PhysRevE.80.056703. Epub 2009 Nov 18.

Abstract

We present microcanonical replica exchange molecular dynamics simulations as an alternative to canonical ones. Its advantage is the easily tunable high acceptance rate for replica exchange. We present the theory, comment on its actual implementation, and demonstrate its application for a common test case, the trp-cage protein.

Publication types

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

MeSH terms

  • Biophysics / methods*
  • Computational Biology / methods
  • Computer Simulation
  • Kinetics
  • Models, Statistical
  • Monte Carlo Method
  • Protein Folding
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Solvents / chemistry

Substances

  • Proteins
  • Solvents