[gmx-users] HBonds with VMD

Marzinek, Jan j.marzinek10 at imperial.ac.uk
Fri Feb 24 22:53:30 CET 2012

Try the representation:
all not water
Then set it to the HBONDS

And refer to the VMD mailing list next time! :)

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Friday, February 24, 2012 9:50 PM
To: Hovakim Grabski; Discussion list for GROMACS users
Subject: Re: [gmx-users] HBonds with VMD

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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