[gmx-users] GridMAT

Justin Lemkul jalemkul at vt.edu
Fri Sep 21 17:20:40 CEST 2012

On 9/21/12 11:16 AM, Shima Arasteh wrote:
> Dear users and admins,
> I'm trying to use GridMAT to get the area per lipid and thickness.
> To do so I ran this command:
> # perl GridMAT-MD.pl param_example
> It doesn't give me any valuable output. This error comes out:
> Generating the grid...
> Your system is bigger in the X-direction
> There are 20 grid points in the X direction, spaced every 0.470368421052632 nanometers
> There are 19 grid points in the Y direction, spaced every 0.480833333333333 nanometers
> Note: the intervals may not be exactly the same in order to have a whole number of grid points
> Analyzing the bilayer...
> The top leaflet "thickness" will be printed to 20x19_top_pbc.dat
> The bottom leaflet "thickness" will be printed to 20x19_bottom_pbc.dat
> The average bilayer "thickness" will be printed to 20x19_average_pbc.dat
> Calculating area per lipid head group...
> Illegal division by zero at GridMAT-MD.pl line 587.
> Would you help me please to get the desired results?

This usually means the atom or residue naming is wrong, the formatting is wrong, 
or some other obscure problem.  Email me (off-list) your input file and 
coordinate file and I will take a look, since this isn't really a Gromacs issue.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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