ArticleJournal of chemical information and modeling2025
GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
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3 authors.
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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.
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