[gmx-users] About atom references calculating area per lipid

Justin Lemkul jalemkul at vt.edu
Fri Nov 18 20:34:47 CET 2016

Again, not really a GROMACS issue and I thought we had this sorted out 
privately, but I'll go ahead and answer here in case it is of general interest.

On 11/18/16 2:05 PM, Poncho Arvayo Zatarain wrote:
> hello: i´m trying to calculate area per lipid of mixed bilayer using Gid-MAT
> for a membrane of 128 DPPC and 128 DPPE and a mixed 128 DPPC+128 DPPE+Drug.
> My atom reference for DPPC is P, so ¿the atom reference for the DPPE need to
> be necesarili the P too?. Because when i run this, the result value of the

The reference atom is the one that you want to define the plane for the APL 
calculation.  It can be anything you want and can even be multiple atoms.

> area per lipid is the same for the mixed membrane and mixed+drug membrane.
> Also, i change the atom reference in DPPE for HS16660 and P for DPPC, this
> according the place occupies by P in DPPC, but the area per lipid is the same
> for mixed membrane and mixed membrane+drug. How i calculate or know my atom
> reference in case i have 2 phospholipids in a mixed bilayer?

Then perhaps your drug isn't doing anything to affect the APL.  The coordinates 
you sent me have very few drug molecules anywhere near the interface, so it is 
unsurprising that APL does not change.



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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