ArticleJournal of chemical theory and computation2025
Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Virtual Screening of Bacteriocins From Lactic Acid Bacteria Against Monkeypox DNA Polymerase: Sakacin P and Mundticin KS Emerge as Promising Candidates.Food science & nutrition · 2026Article
- Surface electrostatic networks control hydrophobic core remodeling in a pH-dependent switching protein.bioRxiv : the preprint server for biology · 2026Article
- Quantifying Small-Molecule Association with Lipid Membranes: Methods, Models, and Limitations.Membranes · 2026Review
- Biomolecular Condensates Act as Distinct Solvation Environments That Reshape Amino Acid pJournal of the American Chemical Society · 2026Article
- A Sequence-Specific Theory for Charge-Regulating IDPs.The journal of physical chemistry. B · 2026Article
- Biomolecular Condensates Act as Distinct Solvation Environments that Reshape Amino Acid pKₐ Values.bioRxiv : the preprint server for biology · 2026Article
- GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.Journal of chemical information and modeling · 2025Article
- Molecular Origins of Simultaneous Chemo-, Enantio-, and Substrate Selectivity in Non-Natural Photoenzymatic Radical Reactions.Journal of the American Chemical Society · 2025Article
- Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method.Journal of chemical theory and computation · 2025Article
- Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation.Journal of chemical theory and computation · 2025Article
- KaMLs for Predicting Protein pJournal of chemical theory and computation · 2025Article
- KaMLs for Predicting Protein pbioRxiv : the preprint server for biology · 2025Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes. Conversely, conformational and environmental changes of the biomolecule affect the protonation state of these groups. With few exceptions, conventional force field-based molecular dynamics (MD) simulations neither account for these effects nor do they allow for coupling to a pH buffer. Here, we present design decisions and applications of a rigorous Hamiltonian interpolation λ-dynamics constant pH method in GROMACS, which rests on GPU-accelerated Fast Multipole Method (FMM) electrostatics. Our implementation supports both CHARMM36m and Amber99sb*-ILDN force fields and is largely automated to enable seamless switching from regular MD to constant pH MD, involving minimal changes to the input files. Here, the first of two companion papers describes the underlying constant pH protocol and sample applications to several prototypical benchmark systems such as cardiotoxin V, lysozyme, and staphylococcal nuclease. Enhanced convergence is achieved through a new dynamic barrier height optimization method, and high p
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.