Data for "High-Performance All-Atom Continuous Constant-pH Molecular Dynamics and Native Asynchronous Replica Exchange in AMBER"

This Zenodo record contains the research data supporting the manuscript “High-Performance All-Atom Continuous Constant-pH Molecular Dynamics and Native Asynchronous Replica Exchange in AMBER” by Guy W. Dayhoff II and Jana Shen. The archive includes simulation input files and starting structures; single-GPU PME-CpHMD and multi-GPU native AREX benchmark data; blocked-tripeptide model-compound validation data; fixed-coordinate thermodynamic-integration data and fitting workflows used to generate updated CpHMD model potentials; HEWL constant-pH validation and structural-analysis data; and the analysis, fitting, and plotting scripts used to produce the reported numerical results and figures. CpHMD titration-coordinate (.lambda) data and processed numerical data underlying the reported protonation-state, pKa, conformational, hydrogen-bonding, hydration, and coupled-site analyses are included. Full Cartesian MD trajectory files were omitted because of their large storage requirements; the retained inputs, titration-coordinate data, processed analysis data, and scripts provide the data needed to reproduce the reported analyses.