Acceleration of the GROMACS Free-Energy Perturbation Calculations on GPUs.

ABSTRACT: Free-energy perturbation (FEP) calculations have emerged as a promising tool for the accurate prediction of ligand binding affinities. However, their widespread adoption in drug discovery pipelines has been hindered by long computation times and complex workflow setups. Here, we introduce an optimized graphics processing unit (GPU)-resident FEP implementation within GROMACS. The GPU-enabled FEP calculations are validated on a benchmark system containing eight ligand-protein pairs, including two charged ligands, on both the Nvidia A100 and the MetaX C500 GPU platforms. The absolute binding free energies predicted on these GPUs show excellent agreement (around 1.0 kcal/mol) with previous CPU-computed results. Compared to a 32-core CPU implementation, the GPU-accelerated FEP calculations demo

SUBMITTER: Chen Y 

PROVIDER: S-EPMC12163693 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature