[gmx-users] local destabilization of bilayer

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 9 15:23:53 CET 2010

afsaneh maleki wrote:
> Hi,
> How do i calculate local destabilization of bilayer?

Define "local destabilization."

>  I can calculate the thickness of the bilayer in the membrane protein 
> with GridMAT-MD but i can't compare it with thickness of pure bilayer. 
> Would you please elaborate it clearly?

The output of GridMAT-MD is a projection of thicknesses across the membrane in 
the x-y dimensions.  You could certainly extract some useful data (i.e., a 
radial plot of thickness) out of the output file using scripting if you wanted. 
  You can use g_dist to get an "average" thickness, i.e. by using a reference 
atom in the "top" and "bottom" leaflets of the bilayer (usually phosphorus). 
The same type of radial measurements could be generated with creative use of 
index groups, trjorder, and g_dist.

> when i calculated thickness of bilayer in membrane protein with 
> GridMAT-MD i do following as:
> ./GridMAT-MD.pl param_example
> perl convert_to_gnuplot.pl <http://convert_to_gnuplot.pl>  
> 20*20_average.dat 20 20
> gnuplot
> splot ' 20*20_average.dat' matrix using(1+$1):(1+$2):3
> set pm3d map
> replot
> but  "20x20_average_pbc.dat" contains a single column of numbers and 400 
> raw line. is it correct?

Yes, per the explanation in our user's guide.


> Thanks very much in advance,
> Afsaneh Maleki


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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