Cyclophilin A (2019) - GROMACS RETIS
====================================

Full-atomistic GROMACS RETIS sampling of the structural rearrangement
(and its rate) of Cyclophilin A and a mutated conformer.

Paper: in preparation.


Files
-----
  retis.rst        PyRETIS 3 input    (pyretisrun -i retis.rst)
  retis.toml       PyRETIS 4 input    (pyretisrun -i retis.toml)
  Orderp.py        order parameter (DeadAng1; needs the mdtraj package)
  gromacs_input/   GROMACS system (conf.g96, topol.top, grompp.mdp,
                   charmm22st.ff/)


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


Status / caveats
----------------
The GROMACS .mdp uses the Verlet cut-off scheme (the group scheme was removed
in GROMACS >= 2020), with PME and force-switched VdW. Confirm it reproduces the
original electrostatics for your GROMACS version before quantitative use.
grompp builds the run and mdrun starts correctly.

The bundled Orderp.py (DeadAng1) 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