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 <[email protected]> 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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