An optimized replica exchange molecular dynamics method.

  • Kamberaj H
  • van der Vaart A
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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.

Author-supplied keywords

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

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  • Hiqmet Kamberaj

  • Arjan van der Vaart

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