[gmx-users] fatal errors regarding grid cells

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 10 00:04:36 CEST 2008

> Hi,
> I am getting this error number of times when I am trying to run Md with 
> a 9 residue peptide in water box using spc216.gro
> It says
> "Number of grid cells is zero. Probably the system and box collapsed."
> earlier after grompp it gives me warning that the protein atom number is 
> less than 10% of total atom number. I dont know if that is causing any 
> problem. even if I change "ns_type" in .mdp file to "simple" from 
> "grid", the problem persists.

Have you searched the mailing list archives?  If you search "number of grid 
cells is zero," you return 70 posts!  Probably one of them will have a clue.

The reason I say this is that you've provided no pertinent details of your 
system - what it contains, how (and if) you prepared, minimized, and 
equilibrated your system.


> Please help.
> Thanks and regards,
> Subhashis
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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