Igor Marques wrote:
chetan,
i'm not sure about the use of -sl option in g_order.
however, for the purpose you mentioned, i'd suggest you to:
create two different trajectories, using trjconv and an index file
grouping lipids closer to the protein and lipids away from the protein.
then, you should be able to analyse each trajcetory and get the order
parameters for each group of lipids.
This is more easily accomplished with trjorder.
-Justin
good luck,
igor
Igor Marques
On Tue, Oct 11, 2011 at 6:20 PM, Poojari, Chetan
<c.pooj...@fz-juelich.de <mailto:c.pooj...@fz-juelich.de>> wrote:
Hi,
I have protein completely inserted into lipid membrane and would
like to study order parameter around the protein as well as away
from the protein.
For this I would like to slice my membrane into parts.
I tried the following command:
g_order -s *.tpr -f *.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -sl 2
The output i get from this is as same as the one where i dont use
-sl 2 flag and it also doesnt show the different parts it has used
for order parameter calculation.
Please can I know how to slice my lipid membrane so that i can study
order parameter for each part separately.
Kind Regards,
chetan
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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
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