H-NS - DNA binding (2019) - GROMACS RETIS
=========================================

RETIS study of the mechanism and rate of the H-NS protein binding to AT-rich
DNA, with GROMACS.

Paper:
  E. Riccardi, E. C. van Mastbergen, W. W. Navarre and J. Vreede,
  "Predicting the mechanism and rate of H-NS binding to AT-rich DNA",
  PLoS Comput. Biol. 15, e1006845 (2019).
  https://doi.org/10.1371/journal.pcbi.1006845


Files
-----
  retis.rst     PyRETIS 3 input    (pyretisrun -i retis.rst)
  retis.toml    PyRETIS 4 input    (pyretisrun -i retis.toml)
  orderp.py     order parameter (CmassDistance; needs the mdtraj package)
  ext_input/    GROMACS system (conf.gro, topol.top, *.itp, grompp.mdp)


Requirements
------------
  * GROMACS (tested with 2021.x)     * the mdtraj Python package


Status / caveats
----------------
This is a large, solvated protein-DNA system. grompp builds the run and mdrun
starts correctly, but a full RETIS run is an HPC-scale effort - it is not
expected to converge on a single workstation in reasonable time.

The bundled orderp.py reads a configuration via "gmx editconf" + mdtraj. It
works on a single-frame configuration but needs updating for how PyRETIS 3/4
hand a trajectory frame (file + frame index) to the order parameter during
path sampling. Update orderp.py to extract the indexed frame before production.


How to run
----------
  PyRETIS 3:   pyretisrun -i retis.rst
  PyRETIS 4:   pyretisrun -i retis.toml