[gmx-users] Bilayer thickness

[Justin Lemkul]

On 10/7/13 8:00 AM, Archana Sonawani-Jagtap wrote:
> Hi,
>
> I have used Grid-Mat program for calculating bilayer thickness and area per
> lipid for POPC bilayer.
>
> For bilayer thickness, without peptide, it provides the lateral area of
> system in angstrom sq. and also APL. (keeping APL as no)
>
> I separately calculated the APL with peptide, It also provides the lateral
> area of system and APL.(keeping thickness as no)
>
> which lateral area has to be considered as the thickness of the bilayer in
> terms of nm? both have different values. I am confused.
>

Lateral area and thickness are different concepts, so I'm not sure what your 
question is.  The thickness values are mostly for plotting purposes, though you 
can average them and get a results reasonably similar to what you would get with 
g_dist.  The APL values are reported individually for every lipid in the output 
file and the average ± std dev is printed to the screen.  In the absence of your 
actual input files and the output produced, there's not much else I can offer to 
help.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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