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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

Journal of chemical information and modeling, 2018-10, Vol.58 (10), p.2043-2050 [Periódico revisado por pares]

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Título:
GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features
Autor: 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
Assuntos: Computer simulation ; Energy ; Energy methods ; Free energy ; Graphics processing units ; Integrated circuits ; Integration ; Interpolation ; Molecular dynamics ; Perturbation
É parte de: Journal of chemical information and modeling, 2018-10, Vol.58 (10), p.2043-2050
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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Descrição: 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.
Editor: United States: American Chemical Society
Idioma: Inglês

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