All files you will need during this tutorial can be downloaded here.

The purpose of each file will be explained closer throughout the tutorial.

[KIGAKI]3 structure file in PDB format: kigaki.pdb
Parameter file for ion addition: ions.mdp
Parameter file for energy minimization: em.mdp
Parameter file for equilibration: eq.mdp
Parameter file for production MD: md.mdp
Bash script for the calculation of distance maps:
Python script for calculating free energies:
Gnuplot file for plotting free energies: plotFES.gnu