Files
All files you will need during this tutorial can be downloaded here.
| [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: | distancemap.sh |
| Python script for calculating free energies: | generateFES.py |
| Gnuplot file for plotting free energies: | plotFES.gnu |