[gmx-users] Illegal divion by zero lipid+protein+solvent

Justin Lemkul jalemkul at vt.edu
Tue Apr 18 14:20:59 CEST 2017

On 4/17/17 5:02 PM, Poncho Arvayo Zatarain wrote:
> Hello gromacs users: I know this question is very common but i have this problem: I´m trying to obtain area per headgropu of a dppc+protein+solvent membrane and when i use GRIDMaAT it appears: illegal division by zero. My coord_file is my gro file, file type is gro, num_frames 1, num lipid types 1, resname 1 is DPPC, atomname 1 is P, resname2 and atomname 2 is none and solvent is TIP3. What could be the problem? Also, i run the same area per headgroup with dppc+solvent (with no protein) using the same atomname and resname and have no error. Or could i use the formula:
> APL = (box_x * box_y) / N_lipids_per_leaflet?

You can't do that if there's a protein.

The error from the program means no lipids were found (zero in the denominator 
of determining the area).  That means your lipid residue name or atom name is 

Please send GridMAT-MD questions to me, off-list, as this is not a GROMACS problem.



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


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