Skip to content

JanaShenLab/CpHMD-Tutorial

Repository files navigation

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

About

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

Topics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages