Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD.

ABSTRACT: Harnessing the power of graphics processing units (GPUs) to accelerate molecular dynamics (MD) simulations in the context of free-energy calculations has been a longstanding effort toward the development of versatile, high-performance MD engines. We report a new GPU-based implementation in NAMD of free-energy perturbation (FEP), one of the oldest, most popular importance-sampling approaches for the determination of free-energy differences that underlie alchemical transformations. Compared to the CPU implementation available since 2001 in NAMD, our benchmarks indicate that the new implementation of FEP in traditional GPU code is about four times faster, without any noticeable loss of accuracy, thereby paving the way toward more affordable free-energy calculations on large biological objects

SUBMITTER: Chen H 

PROVIDER: S-EPMC7686227 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature