ArticleJournal of chemical theory and computation2017
Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed.
- Estimating Permeabilities from Biased Molecular Dynamics with a Green-Kubo Formalism for Transport across the Blood-Brain Barrier.Journal of chemical information and modeling · 2026Article
- "Air-Lock" gating mechanism of CsoS1D for metabolite translocation through the α-carboxysome shell.Plant physiology · 2026Article
- Electrostatic tuning of the pyridoxal-5'-phosphate cofactor site defines pH dependence in type I cystathionine β-lyases.The Journal of biological chemistry · 2026Article
- Microenvironmental pH and host-pathogen co-evolution potentially influence the structural architecture of junctional adhesion molecules.Molecular genetics and genomics : MGG · 2026Article
- pH-Driven βACS omega · 2026Article
- Graph-Based Deep Learning Models for Predicting pJournal of chemical information and modeling · 2026Article
- GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.Journal of chemical information and modeling · 2025Article
- Insights into the Catalytic Activity of a Metagenome-Derived Urethanase.Journal of the American Chemical Society · 2025Article
- PKAD-R: curated, redesigned and expanded database of experimental pKa values in proteins.Journal of computational biophysics and chemistry · 2025Article
- Simulating Biomolecules with the Variable Protonation State: A Tutorial for Constant-pH Molecular Dynamics in NAMD.The journal of physical chemistry. B · 2025Article
- Effect of pH, Temperature, Molecular Weight and Salt Concentration on the Structure and Hydration of Short Poly(Polymers · 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
- Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications.Journal of chemical theory and computation · 2025Article
- pH-Dependent Assembly and Stability of Toll-Like Receptor 3/dsRNA Signaling Complex: Insights from Constant pH Molecular Dynamics and Metadynamics Simulations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Force Field Limitations of All-Atom Continuous Constant pH Molecular Dynamics.The journal of physical chemistry. B · 2024Article
- Hybrid neMD/MC lipid swapping algorithm to equilibrate membrane simulation with thermodynamic reservoir.The Journal of chemical physics · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Allosteric coupling of substrate binding and proton translocation in MmpL3 transporter frommBio · 2024Article
- Proline substitutions in the ASIC1 β11-12 linker slow desensitization.Biophysical journal · 2024Article
31 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
8 authors.
Funding
Abstract
An increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementation of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.
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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 OpenQuestion graph.