[gmx-users] HBonds with VMD

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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