[gmx-users] area per lipid

Justin A. Lemkul jalemkul at vt.edu
Mon Dec 7 17:36:19 CET 2009

nittopuran natya wrote:
> Dear gromacs users,
> I am trying to calculate and generate the xvg output of area per lipid 
> for drug molecules inserted into the DMPC 128 lipid bilayer. I have run 
> the simulation for 200 ns. First 100 ns were discarded as equilibration. 
> The next 100 ns I will use for determining area per lipid. I have short 
> tarjectory file .trr and .xtc (20 ns of each). Could someone pls tell me 
> how can i generate a xvg plot for area per lipid as a function of time 
> evolution with using these 20 ns short trajectory over the last 100 ns 
> in one xvg plot . Which gromacs utility I have to use? And also how to 
> calculate the area per lipid.

There is no straightforward way to do this, especially if your drug molecules 
are occupying some of the interfacial lateral area of the lipids.  How does one 
then separate the lateral are contributed by the drugs from the lateral area 
contributed by a lipid?  We developed a program in our lab to address such 
difficult systems, and you can read about it here (as well as the related 


At the moment, it can only analyze single coordinate files, not trajectories, 
but it may yet prove useful for you.



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


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