[gmx-users] Constraining hydrogen - heavy atom bonds with different naming.

Dawid das addiw7 at googlemail.com
Tue Mar 1 19:24:53 CET 2016

Dear Gromacs Experts,

I am pretty sure I have already answered this question long time ago but I
cannot find
it. What I did is I added a new residue for my system and it contains
hydrogen atoms.
Now, the thing is that all atoms names start with "M", so I have MH21,
MH22, MCA1, etc.
atoms. I want to constrain hydrogen - heavy atom bonds:

constraints   = h-bonds

and I am not sure whether I constraint those novel hydrogens.  In other
words, how does
Gromacs 5.0.4 know that my atom is a hydrogen? Based on atomic number in
ffnonbonded.itp or based on atom name/type?

Best wishes,
Dawid Grabarek

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