ArticleJournal of chemical theory and computation2022
Scalable Constant pH Molecular Dynamics in GROMACS.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Bridging the accuracy-speed divide in reactive molecular dynamics with QuantaMind MD.Science advances · 2026Article
- A multiscale modeling framework for transport of PEGy-lated lipid nanoparticle through the extracellular matrix.bioRxiv : the preprint server for biology · 2026Article
- Membrane environment sets the functional pKBiophysical journal · 2026Article
- Kinase inhibitors can change protonation or tautomeric state upon binding.bioRxiv : the preprint server for biology · 2026Article
- Quantifying Small-Molecule Association with Lipid Membranes: Methods, Models, and Limitations.Membranes · 2026Review
- Implementation and Validation of Titratable Cysteine in GROMACS-Based Constant-pH Molecular Dynamics.Journal of chemical theory and computation · 2026Article
- pH-dependent activation of the NaNature communications · 2026Article
- Mitigating alkaline instability induced by tyrosine-tyrosine repulsion in an FcγRIIIa-binding protein through phenylalanine substitution.Journal of biochemistry · 2026Article
- Multiscale Structural Elucidation of Vitrinite and Inertinite in Tar-High Coal: A Combined Characterization via FTIR,ACS omega · 2026Article
- Mining of natural diversity enables efficient and expressible peptide asparaginyl ligases.Nature communications · 2026Article
- A Sequence-Specific Theory for Charge-Regulating IDPs.The journal of physical chemistry. B · 2026Article
- KIMMDY: a biomolecular reaction emulator.Nature communications · 2026Article
- From Membrane Composition to Antimicrobial Strategies: Experimental and Computational Approaches to AMP Design and Selectivity.Small (Weinheim an der Bergstrasse, Germany) · 2026Review
- Decoding pH-Driven Phase Transition of Lipid Nanoparticles.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Phosphorylation induces altered protonation states and allosterically regulates Rac1-RhoGDI complex.Protein science : a publication of the Protein Society · 2026Article
- Exploring the Potential Molecular Targets of Cyanidin-3-O-glucoside for Type 2 Diabetes Mellitus Treatment.Endocrine, metabolic & immune disorders drug targets · 2026Article
- A Computational Modeling for Reconfigurable Biosensors.BioNanoScience · 2026Article
- Structural insights into AQP3 channel closure upon pH and redox changes reveal an autoregulatory molecular mechanism.Nature communications · 2025Article
- GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.Journal of chemical information and modeling · 2025Article
- Structure-Based Modeling of Environment-Dependent Protonation States Across LNP Formulations with Atomistic CpHMD.Molecular pharmaceutics · 2025Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L.
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