Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems.

Fass, Josh; Sivak, David A; Crooks, Gavin E; Beauchamp, Kyle A; Leimkuhler, Benedict; Chodera, John D

Fass, Josh; Sivak, David A; Crooks, Gavin E; Beauchamp, Kyle A; Leimkuhler, Benedict; Chodera, John D.

Afiliação

Fass J; Tri-Institutional PhD Program in Computational Biology & Medicine, New York, NY 10065, USA.
Sivak DA; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Crooks GE; Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
Beauchamp KA; Rigetti Computing, Berkeley, CA 94710, USA.
Leimkuhler B; Counsyl, South San Francisco, CA 94080, USA.
Chodera JD; School of Mathematics and Maxwell Institute of Mathematical Sciences, James Clerk Maxwell Building, Kings Buildings, University of Edinburgh, Edinburgh EH9 3FD, UK.

Entropy (Basel) ; 20(5)2018 May.

Article em En | MEDLINE | ID: mdl-30393452

Palavras-chave

BAOAB; Bussi-Parrinello; KL divergence; Langevin dynamics; Langevin integrators; integrator error; molecular dynamics integrators; nonequilibrium free energy; sampling error; shadow work; velocity verlet with velocity randomization (VVVR)

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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2018 Tipo de documento: Article

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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2018 Tipo de documento: Article