[gmx-users] Number of grid cells is zero

[Tsjerk Wassenaar]

Hi Alif,

You seem to be one of a number of people suffering crashes with
non-standard systems. Still, I suspect this is not (yet?) a Gromacs
problem, but rather reflecting that the topology is bad. Where did you
get it from? Did you check it, and how? What procedure did you use so
far?

Best,

Tsjerk

On 3/14/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> best alep wrote:
> > Hi Dr. Dallas,
> >
> > Thanks for replying my mail, I've already seen the trajectory file.
> > There's no structure.. I saw only dots.. these dots were not connected
> > with each other. But the colors shows the difference of the atoms
> > (probably). What is happening? Can you or anyone help me please? I'm new
> > to this (molecular simulation)..so my basic is not strong. Is it
> > concerning my simulation box? or my mdp file?..By the way, I'm trying to
> > run simulation on Oleyl oleate C36 O2 structure.
> >
> > Clues, or comments or advices please...
> >
> your starting structure is bad. fix it with minimization etc.
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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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