GROMACS version: 2020.6
GROMACS modification: No
We want to have a list of all the contacts between two proteins within a 0.5 nm cutoff.
If we want to use the -contact option of gmx hbond we should change the -r flag (0.5 instead of the 0.35 default) and not use the flag -r2, are we right?
In other words, if we are interested in all kind of contacts, leaving -r = 0.35 would be meaningless because this cutoff is specific for h-bonds interaction…
This is what we understood.
we are using this command:
gmx hbond -s .tpr -f .xtc -n .ndx -g hbond_ref.log -hbn hbindex_ref.ndx -contact -r 0.5
any comment would be helpful.