[gmx-users] GRID-MAT- area per lipid calculation

[Justin Lemkul]

On 7/11/16 3:21 AM, amitbehra at chemeng.iisc.ernet.in wrote:
> Hello Justin,
> I was trying to calculate area per lipid using GridMAT. But its giving
> back me the error :
> " Illegal division by zero at GridMAT-MD.pl line 761 "
> Can you help in finding the root of this error ? The bilayer just consists
> of one type of lipid and sol.
>

This error means no lipids were identified in the calculation.  Your 
specification of the residue name or identifying atom(s) is incorrect.

But the larger point is that (while I like to see people use software I've 
developed), you don't need it.  For a pure membrane,

APL = (box_x * box_y) / N_lipids_per_leaflet

You can get the box vectors from the .edr file and script a simple calculation 
for each frame.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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