[gmx-users] Number of grid cells is zero

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 14 09:14:21 CET 2007

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



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

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