[gmx-users] Re: gmx-users Digest, Vol 67, Issue 89

[Алексей Раевский]

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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