{"doi":"10.1021/acs.jcim.5c02162","title":"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.","journal":"Journal of Chemical Information and Modeling","year":2025,"id":549300,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9497,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":98029,"name":"Christophe Chipot","orcid":"0000-0002-9122-1698","position":1,"is_corresponding":false},{"id":56693,"name":"Benoı̂t Roux","orcid":"0000-0002-5254-2712","position":2,"is_corresponding":false},{"id":1443502,"name":"Sarah Moe","orcid":"0009-0009-1528-7079","position":0,"is_corresponding":true}],"reference_count":86,"raw_metadata":null,"created_at":"2026-07-19T02:54:07.823422Z","pmid":"41364919","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}