GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.

ABSTRACT: We introduce a GPU-based implementation of the hybrid nonequilibrium molecular dynamics-Monte Carlo constant-pH simulation method within the NAMD package. Benchmark results demonstrate that the new implementation achieves a substantial speedup over its CPU-based counterpart, while preserving the same level of accuracy. This performance gain expands the practical applicability of pH-controlled, all-atom simulations across a wide range of biomolecular systems. Although exhaustive enumeration of all possible protonation-state combinations remains a major challenge within conventional molecular dynamics frameworks, the ability to simulate at a defined pH─combined with GPU-acceleration─offers a powerful and efficient means for investigating dynamic protonation profiles of biomolecules.

SUBMITTER: Moe S 

PROVIDER: S-EPMC12756948 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature