[gmx-users] HBonds with VMD
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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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