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CpHMD-Tutorial: A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM

Methods covered in this tutorial [v1.0]

  • CPU Hybrid-solvent CpHMD in CHARMM: Wallace JA, Shen J. Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange. J. Chem. Theory Comput. 7: 2617–2629, 2011. https://doi.org/10.1021/ct200146j

  • CPU Membrane-enabled Hybrid-solvent CpHMD in CHARMM: Huang YD, Chen W, Dotson DL, Beckstein O, and Shen J. Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA. Nat Commun 7: 12940, 2016. https://doi.org/10.1038/ncomms12940

  • CPU All-atom PME CpHMD in CHARMM: Huang Y, Chen W, Wallace JA, Shen J. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water. J. Chem. Theory Comput. 2016; 12: 5411–5421. https://doi.org/10.1021/acs.jctc.6b00552

  • CPU GBNeck2 implicit-solvent CpHMD in Amber: Huang Y, Harris RC, Shen J. Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis. J. Chem. Inf. Model. 58: 1372–1383, 2018. https://doi.org/10.1021/acs.jcim.8b00227

  • GPU GBNeck2 implicit-solvent CpHMD in Amber: Harris RC and Shen J. GPU-accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single pH Simulations. J. Chem. Inf. Model. 59: 4821-4832, 2019. https://doi.org/10.1021/acs.jcim.9b00754

Codes for all examples in this tutorial: https://gitlab.com/shenlab-amber-cphmd/cphmd-tutorial

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Github repository for the LiveCoMS tutorial of the continuous constant pH molecular dynamics method

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