ArticleJournal of chemical theory and computation2025
Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method.
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 4 papers.
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4 citing papers in PubMed.
- Quantifying Small-Molecule Association with Lipid Membranes: Methods, Models, and Limitations.Membranes · 2026Review
- Constant-pH Molecular Dynamics of Cationic Peptide Dendrimers Binding to siRNA.Journal of chemical information and modeling · 2026Article
- Clock-Turning Control of P450 TxtE Regioselectivity Enables Precise Site Functionalization of Aromatic Compounds.JACS Au · 2026Article
- Investigating the potential mechanism of bisphenols on neurodegeneration through network toxicology and molecular docking.NAM journal · 2025Article
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3 authors.
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Abstract
Incorporating pH into molecular dynamics simulations is vital for accurately capturing the fully coupled conformational, energetic, and protonation landscape of many systems. The constant-pH molecular dynamics (CpHMD) methodologies represent state-of-the-art approaches to achieve this, with stochastic titration CpHMD (st-CpHMD) currently being one of the most well-developed and validated methods. St-CpHMD is already compatible with both the GROMOS 54A7 and CHARMM 36m force fields, and we extend it here to support the AMBER 14SB force field available in the GROMACS software package. We introduce and validate a minor modification to the official atomic partial charges of ff14SB (to achieve neutralization of the main chain) to render them compatible with st-CpHMD, and we benchmark the final implementation using lysozyme and Staphylococcal nuclease proteins. Although the root-mean-square error (RMSE) values of the predictions for p
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