[gmx-users] Bilayer thickness
jalemkul at vt.edu
Mon Oct 7 14:06:09 CEST 2013
On 10/7/13 8:00 AM, Archana Sonawani-Jagtap wrote:
> 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
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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