gmxapi-scripts

Sample scripts for running some high-level tasks including ensemble simulation in gmxapi.

As of 2022, we recommend using https://github.com/kassonlab/gmxapi-tutorials as the entry point for learning and demonstrating gmxapi.

These scripts demonstrate 2019 and planned functionality under subtasks of GROMACS issue 2045 and as outlined in the roadmap

The general syntax for the gmxapi user interface in GROMACS 2020 will be finalized by about May 1, 2019. Please note feedback, questions, and concerns in the Issues or to issues@gmxapi.org.

Examples

brer.py

BRER simulation-analysis protocol implemented as a gmxapi script, with a Python analysis module (brer_tools.py not implemented here) and C++ MD extension code (myplugin.so also not shown).

restrained_ensemble.py

Restrained ensemble example script using restraint potentials implemented in myplugin (not shown) and analysis code expressed in restrained_md_analysis.py.

rmsf.py

Run simulations with a range of tau-t values and analyze with the gmx rmsf tool.

run_adaptive_msm.py

Use custom analysis code from analysis.py to set the initial conformations for iterations of simulation batches.