Here there are the MDP files for the alchemical transforamations for the complex and the ligand

There is also an example SBATCH script. This script uses a job array to implement the transformations but a -multidir setup can also be used

If you are using HPC_Drug (https://github.com/MauriceKarrenbrock/HPC_Drug/) the fsdam_input.py script will automatically generate a RESTART directory by extracting the HREM conformations from the TRR file (in fact I wrote less frames in the TRR as in the XTC in order to be sure that each extracted frame is decorrelated from the others)
It will also create some scripts to generate the TPR files, but if you are using the Loose-Tight restraint do not use them but generate a new script with the script given in bin/
If you are generating the ligand in a box of water the script will automatically add the water to the frames of the ligand in vacuum (all molecules must be whole)

Later on to get the free energy values use the fsdam_postprocessing.py script from HPC_Drug

