[gmx-users] GridMAT

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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