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
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
