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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.
Lee, Tai-Sung; Cerutti, David S; Mermelstein, Dan; Lin, Charles; LeGrand, Scott; Giese, Timothy J; Roitberg, Adrian; Case, David A; Walker, Ross C; York, Darrin M.
Afiliação
  • Lee TS; Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States.
  • Cerutti DS; Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States.
  • Mermelstein D; Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States.
  • Lin C; Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States.
  • LeGrand S; A9.com , Palo Alto , California 94301 , United States.
  • Giese TJ; Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States.
  • Roitberg A; Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States.
  • Case DA; Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States.
  • Walker RC; GlaxoSmithKline PLC , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States.
  • York DM; Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States.
J Chem Inf Model ; 58(10): 2043-2050, 2018 10 22.
Article em En | MEDLINE | ID: mdl-30199633
ABSTRACT
We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and free energy methods in Amber18. Of particular interest is the development of alchemical free energy algorithms, including free energy perturbation and thermodynamic integration methods with support for nonlinear soft-core potential and parameter interpolation transformation pathways. These methods can be used in conjunction with enhanced sampling techniques such as replica exchange, constant-pH molecular dynamics, and new 12-6-4 potentials for metal ions. Additional performance enhancements have been made that enable appreciable speed-up on GPUs relative to the previous software release.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Simulação de Dinâmica Molecular Idioma: En Ano de publicação: 2018 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Software / Simulação de Dinâmica Molecular Idioma: En Ano de publicação: 2018 Tipo de documento: Article