ArticleJournal of chemical theory and computation2014
Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Benchmark Study for Calculations of pKa Values of Metal Ligands in Proteins.Journal of chemical theory and computation · 2026Article
- Real-Time Visualisation of Reaction Kinetics and Dynamics: Single-Molecule Insights into the Iminium-Catalysed Diels-Alder Reaction.Angewandte Chemie (International ed. in English) · 2025Article
- PKAD-R: curated, redesigned and expanded database of experimental pKa values in proteins.Journal of computational biophysics and chemistry · 2025Article
- Evaluating the protonation state of the catalytic Cys25 in cruzain cysteine protease: A target for Chagas disease.Protein science : a publication of the Protein Society · 2025Article
- Simulating Biomolecules with the Variable Protonation State: A Tutorial for Constant-pH Molecular Dynamics in NAMD.The journal of physical chemistry. B · 2025Article
- Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method.Journal of chemical theory and computation · 2025Article
- apoCHARMM: High-performance molecular dynamics simulations on GPUs for advanced simulation methods.The Journal of chemical physics · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- A pH-Dependent Coarse-Grained Model for Disordered Proteins: Histidine Interactions Modulate Conformational Ensembles.The journal of physical chemistry letters · 2024Article
- Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions.Journal of chemical theory and computation · 2024Article
- Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations.Journal of chemical theory and computation · 2024Article
- phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS.Journal of chemical information and modeling · 2024Article
- Ion channel selectivity through ion-modulated changes of selectivity filter pProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Constant pH molecular dynamics simulations: Current status and recent applications.Current opinion in structural biology · 2022Review
- Increasing the Realism ofJournal of chemical theory and computation · 2022Article
- Extending the Stochastic Titration CpHMD to CHARMM36m.The journal of physical chemistry. B · 2022Article
- Scalable Constant pH Molecular Dynamics in GROMACS.Journal of chemical theory and computation · 2022Article
- Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier.Journal of chemical information and modeling · 2022Article
- Protein pJournal of chemical theory and computation · 2022Article
- Prediction of protein pChemical science · 2022Article
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Authors and funding
4 authors.
Funding
Abstract
We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter
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Registered trials
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 OpenQuestion graph.