[gmx-users] About Area per lipids in Mixed Membranes

[Justin Lemkul]

On 11/15/16 2:29 PM, Poncho Arvayo Zatarain wrote:
>
>
> Hello: I want to calculate the area per lipids in DPPC/DPPE membranes of 128
> lipids per leafleft. I have a membrane with 128 DPPC and 128 molecules ofDPPE
> and Box X and Box Y are 8.846591 and 8.846591 respectivelly. Should i
> calculate the area per lipid using (Box X * Box Y)/(#lipids per leafleft)?

That assumes the contributions to the area are equal between the two lipids, 
which may not be correct.  There are methods for estimating the contribution of 
each lipid to the APL, though, e.g. http://www.bevanlab.biochem.vt.edu/GridMAT-MD/

> Also i have tha same membrane (128 molecules of DPPC and 128 molecules of
> DPPE) but with more than 50 molecules of a drug inside the membrane. Box X
> and Box Y are 9.118480 and 9.118480. Should i use Box X * Box Y)/(#lipids per
> leafleft) too? I´m using gromacs 5.0.2

No, because the drug may occupy some portion of the membrane surface that has to 
be accounted for.  The above program will do that if set up properly.

-Justin

-- 
==================================================

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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