[gmx-users] image control

[Tsjerk Wassenaar]

Hi Myunggi Yi,

I said link them, not mail them to me. Check your .tpr file to see 1.
whether these parts of your lipids are already separated at the start of the
equilibration run (you can extract the coordinates with editconf) and 2.
whether you actually have bonds defined where you expect them to be.

Cheers,

Tsjerk

On Jan 16, 2008 3:47 PM, Myunggi Yi <myunggi at gmail.com> wrote:

> I have tried to attach my .gro file, but it is not allowed in mailing
> list.
> I'm attaching small file of the snap shot of the gro file.
> The limit is 50 KB. What can I do?
> I'm attaching the file to you (Tsjerk Wassenaar).
> Again I didn't do any modification.  This is a just output from MD.
> As you know you can check the coordinate in the .gro text file.
> This is not a visulalization problem.
> If any body wants, I will send you my .gro file.
>
> I downloaded popc.itp form Dr. Tieleman's web.
>
> As you see the lipid can be broken any bond (see two fragment of lipid at
> the bottom),
> however the left sile lipid are Okay.
> Any idea?
>
>
> On Jan 16, 2008 7:47 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> > 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.
> >
> > Tsjerk
> >
> >
> > 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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>
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
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> Institute of Molecular Biophysics
> Florida State University
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>
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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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