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Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration.

  • Author(s): Fajer, Mikolai
  • Hamelberg, Donald
  • McCammon, J Andrew
  • et al.

Published Web Location

https://doi.org/10.1021/ct800250m
Abstract

Accelerated molecular dynamics (AMD) is an efficient strategy for accelerating the sampling of molecular dynamics simulations, and observable quantities such as free energies derived on the biased AMD potential can be reweighted to yield results consistent with the original, unmodified potential. In conventional AMD the reweighting procedure has an inherent statistical problem in systems with large acceleration, where the points with the largest biases will dominate the reweighted result and reduce the effective number of data points. We propose a replica exchange of various degrees of acceleration (REXAMD) to retain good statistics while achieving enhanced sampling. The REXAMD method is validated and benchmarked on two simple gas-phase model systems, and two different strategies for computing reweighted averages over a simulation are compared.

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