[gmx-users] HBonds with VMD

Marzinek, Jan j.marzinek10 at imperial.ac.uk
Fri Feb 24 22:31:18 CET 2012

Dear GROMACS users,
I'm a novice user,
I've been trying to find a way to visualize hydrogen bonds with VMD,but  I haven't been successful.
After running a simulation  of 13 Hypericin molecules solved in Water, I loaded the.gro file and then the trajectory file .xtc, after that in the Create Representation window I changed to CPK and then modified to show just the Hypericin molecules (not water).Later I created another representation and changed to HBONDS and in the panel  changed to "name H O",but VMD doesn't show the HBONDS formed between O and H atoms.
Where is my mistake?
Thanks in Advance

Hovakim Grabski
Russian-Armenian(Slavonic) University

I think you should refer to VMD mailing list. However, as far as I know you should create representation:
all not water
and set to HBONDS


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