[gmx-users] image control

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jan 16 13:47:36 CET 2008

Hi Myunggi Yi,

In addition, it may help if you give some examples: link the structure file,
the topology file, and some sample images highlighting the point your trying
to make. Apparently, leaving us guessing doesn't help.


On Jan 16, 2008 12:10 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> Myunggi Yi wrote:
> > Thank you.
> >
> > I know general setup to run a simulation, and I'm running one.
> > As you see the title, I have problem with image.
> Well that was a dozen emails ago and we've talked about many topics
> since. You'll get nowhere fast by assuming that the people you're asking
> for help have the whole email exchange memorized... they have their own
> problems. To get effective help, describe things fully, and if you need
> to refer back to something, go and get a URL to the mailing list
> archives on the GROMACS webpage. This may seem onerous, but you're the
> one trying to get free help, so you maximise your chances by making life
> easier on the people who might give it to you.
> > I'm getting broken lipid in the trajectory.
> You're not. mdrun doesn't write broken molecules if they were whole in
> the topology. Your visual representation might have them crossing PBC
> boundaries in a way that might make them look broken, however. There are
> many ways to adjust your visual representation, however.
> > Would you let me know how to avoid this?
> As someone else has already suggested, judicious use of trjconv and the
> .gro file you use with VMD are needed here. Read the man page for
> trjconv and experiment to find what works for whatever your trying to do.
> > Do I need special setup?
> No
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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