Sample input scripts and analysis scripts for use alongside the models on Zenodo (https://doi.org/10.5281/zenodo.4415835)
Forcefields used: CHARMM 36 (toppar_c36_jul17)
Files included:
Input files:
protein_input.namd - This is the namd run script with all the MD parameters included, as used for the apoferritin containing system, edit as required
submit_namd.sh - This is an example submit script used for submission to ARCHER2 with the required resources to run MD of the apoferritin system
Analysis files:
coor2pdb.tcl - This is the tcl script used for converting the VMD binary output coor file into a pdb file. Intended for use through vmd without the GUI
watertracker.py - This is the python script used for tracking the internal waters in the hollow centre of the apoferritin molecule. MDAnalysis required
Energy_Time.ipynb - This jupyter notebook reads in a text file of total energies and writes the plot
Density_Time.ipynb - This jupyter notebook reads in a text file of system volumes, converts to density, and writes the plot
write_smallbox.py - This is the python script for selecting a smaller cube of water from the final frame of the larger 645 Angstrom trajectory and writing it to pdb format
rdf.py - This python script plots the RDF for water using the pdb written out from write_smallbox.py