[gmx-users] HBonds with VMD

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 24 22:50:29 CET 2012

Hovakim Grabski wrote:
> 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?

Probably the atom names are wrong.  This is a VMD question, so you're better off 
posting to the VMD mailing list for help on such topics.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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