GROMACS modification: Yes/No
Here post your question I am seeking some suggestions or help on how to find the distance between the different protein residues and ligand molecules as a function of time. I am seeing some suggestions regarding making index file of all the four residues of the protein and group it with the ligand but it did not work for me. Also for the index file do I consider the em. gro file or the output trajectory file (.xtc, or center.xtc or fix.xtc)
As I can see some other people also having trouble with the same issue a detailed explanation may also help others too.