[gmx-users] local destabilization of bilayer

[Justin A. Lemkul]

afsaneh maleki wrote:
> Hi,dear justin,
> 
> thanks for your reply
> 
> The local destabilization  is the subtraction of the thickness of the 
> bilayer in the membrane protein with  thickness of bilayer in the pure 
> bilayer.
> 
> 

Well, you can certainly get that from the GridMAT-MD output.  That's one of the 
reasons we designed it.  See the previous post for specifics.

-Justin

> 
> 
> 
> 
> On Tue, Mar 9, 2010 at 5:53 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <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.
> 
>     -Justin
> 
> 
> 
>         Thanks very much in advance,
>         Afsaneh Maleki
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================