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

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...

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Detalles Bibliográficos
Autores principales: Fajer, Mikolai, Hamelberg, Donald, McCammon, J. Andrew
Formato: Texto
Lenguaje:English
Publicado: American Chemical Society 2008
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651661/
https://www.ncbi.nlm.nih.gov/pubmed/19461870
http://dx.doi.org/10.1021/ct800250m
Descripción
Sumario: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.