[gmx-users] HBonds with VMD

[Marzinek, Jan]

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

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

Jan
________________________________________
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

--
========================================

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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