[gmx-users] local destabilization of bilayer

[afsaneh maleki]

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.






On Tue, Mar 9, 2010 at 5:53 PM, Justin A. Lemkul <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>
>>  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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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