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
