cpAEDS

Pipeline tool to set up constant pH simulations with Gromos using AEDS.

cpAEDS automates the complete constant-pH molecular dynamics workflow: setup of GROMOS AEDS input files, job submission, parallel post-processing, and exponential reweighting for pH-curve reconstruction from single simulations without running a full titration series.

Workflow

settings.yaml → SetupSystem → GROMOS MD → postprocessing_parallel → reweighting → plots

1. Setup: generate per-offset run folders and GROMOS input files
2. Run: submit SLURM/bash jobs; monitor with check_runs
3. Post-process: extract energies and free energies in parallel
4. Reweight: reconstruct protonation fractions at arbitrary EIR offsets using reweighting_constpH / parallel_reweight
5. Plot: StdPlot for offset-vs-fraction, ReweightPlot for titration curves

See docs/getting_started.rst for a full usage guide.

Copyright

Copyright (c) 2022, Benedict Braunsfeld

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.6.