ArticleJournal of chemical information and modeling2024
phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS.
Article in Journal of chemical information and modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Membrane environment sets the functional pKBiophysical journal · 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
- Direct evidence of acid-driven protein desolvation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Decoding pH-Driven Phase Transition of Lipid Nanoparticles.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Lipid Nanoparticle Database towards structure-function modeling and data-driven design for nucleic acid delivery.Nature communications · 2026Article
- Mechanisms of light harvesting complex proteins in photoprotection of the brown tide alga.Nature communications · 2025Article
- Structure-Based Modeling of Environment-Dependent Protonation States Across LNP Formulations with Atomistic CpHMD.Molecular pharmaceutics · 2025Article
- Molecular simulations meet personalized medicine: The mechanism of action of CLC-5 antiporter and the origin of Dent's disease.PNAS nexus · 2025Article
- Constant-pH Simulation of the Human βJournal of chemical information and modeling · 2025Article
- Revealing pH-dependent antimicrobial peptide, GL13K, characteristics: A constant pH molecular dynamics study.bioRxiv : the preprint server for biology · 2025Article
- Predicting residue ionization of OmpF channel using Constant pH Molecular Dynamics as benchmark.PLoS computational biology · 2025Article
- Challenges and opportunities in computational studies for lipid nanoparticle development.npj drug discovery · 2025Review
- Structure-based rational design of covalent probes.Communications chemistry · 2025Review
- Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method.Journal of chemical theory and computation · 2025Article
- A highly stable monomeric red fluorescent protein for advanced microscopy.Nature methods · 2025Article
- A constant pH molecular dynamics and experimental study on the effect of different pH on the structure of urease from Sporosarcina pasteurii.Journal of molecular modeling · 2025Article
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5 authors.
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Abstract
Constant pH molecular dynamics (MD) is a powerful technique that allows the protonation state of residues to change dynamically, thereby enabling the study of pH dependence in a manner that has not been possible before. Recently, a constant pH implementation was incorporated into the GROMACS MD package. Although this implementation provides good accuracy and performance, manual modification and the preparation of simulation input files are required, which can be complicated, tedious, and prone to errors. To simplify and automate the setup process, we present phbuilder, a tool that automatically prepares constant pH MD simulations for GROMACS by modifying the input structure and topology as well as generating the necessary parameter files. phbuilder can prepare constant pH simulations from both initial structures and existing simulation systems, and it also provides functionality for performing titrations and single-site parametrizations of new titratable group types. The tool is freely available at www.gitlab.com/gromacs-constantph. We anticipate that phbuilder will make constant pH simulations easier to set up, thereby making them more accessible to the GROMACS user community.
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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.