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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

2018; American Chemical Society; Volume: 58; Issue: 10 Linguagem: Inglês

10.1021/acs.jcim.8b00462

1549-960X

Tai‐Sung Lee, David S. Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand, Timothy J. Giese, Adrián E. Roitberg, David A. Case, Ross C. Walker, Darrin M. York,

Quantum, superfluid, helium dynamics

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.