Sorry for so disordered questions... <3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group.>
The problem is that I don't know how to create index group (like "protein" or "non-protein"), cause I have to unite H2O (the most close to the carbonyl carbon) and the carbonyl carbon of valyn, just an atom not full residue. So I don't understand how to identify this atom for gromacs...by number of atom in whole structure or something else? P.S. about the list of functions in mdp I sent you, I wanted to be sure I have chosen everything I had to...according to the article... Thank you very much, sory for disturb.
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