[gmx-users] calculate area per lipid and bilayer thickness versus time

Justin Lemkul jalemkul at vt.edu
Tue Jan 22 14:05:51 CET 2013

On 1/22/13 12:00 AM, Kieu Thu Nguyen wrote:
> Thank Justin ! And i used GridMAT-MD as you advised.
> I got result "The average bilayer "thickness" will be printed to
> 50x50_average_pbc.dat". But that result is only equal to a half of
> experiment result. I think "bilayer thickness" is equal to the sum of "top
> leaflet thickness" and "bottom leaflet thickness". So should i double "The
> average bilayer "thickness"..." mentioned above ?

No.  The program measures the total thickness, using the reference atoms you 
provide.  The individual files ("top thickness" and "bottom thickness") 
represent two ways of measuring the same thing, using both leaflets as 
reference, which are then averaged to produce the desired distance file.  Please 
refer to our paper for the algorithm.

> And i do not get average area per lipd, just "The average area per lipid in
> the top leaflet is 64.2329395973154 sq. Angstroms. The average area per
> lipid in the bottom leaflet is 63.3821721854305 sq. Angstroms".

The data file contains areas for each individual lipid, which can be averaged.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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