Enclosed are scripts used for analyzing MD simulations of PS II in python. Below is a brief description:
Contains relevant .pdb, .dat, .pkl etc. files used in this work. These are all necesary for the .ipynb files under the scripts directory
Several .ipynb files are enclosed which exhibit a range of functionalities, currently including the following:
- Script for checking temperature and pressure of a simulation
- Script for comparing geometry of active site in simulation to reference structure
- Script for generating .gro and .top files
- Script for map-based Hydrogen bonding analysis
- Script for computing recall of crystallographic waters in water channels as well as around the active site
- Script for computing distance of randomly selected bulk waters to active site
Topology folder for this work
.pdb file contaning coordinates of additional waters from the simulation which are likely to be in the PS II S1 structure (within 20 Angstrom of OEC)
reference PS II structure used for this work - can be loaded up in Coot and overlaid with strong_peaks_in_20_angstrom_of_OEC.pdb for comparison