Poojari, Chetan wrote:
Thank you Justin, Igor for your suggestions.
I tried with trjorder and below is the command i used:
trjorder -f *.xtc -s *.tpr -n order.ndx -na 50 -da 0 -r 0.5 -o ordered.xtc
I choose protein as my reference group and lipids as the group of molecules
to be ordered, -na 50 : no of atoms in lipid molecule and cut-off distance
of 0.5nm from protein.
As i understood from trjorder description, the above command i have used
should order lipids within 0.5nm from the protein and this information will
be outputted into new xtc file i am writing. Using the new xtc file with
g_order i should be able to calculate order parameter for lipids within 0.5nm
from protein. Please can I know if I am right with the understanding of the
trjorder description.
All the lipids are ordered, not just the ones within 0.5 nm. The -r option is
only useful in conjunction with -shell, for printing the molecules within the
specified distance. Here, it's not doing anything.
Is it possible to order the lipids away from the protein using trjorder, so
that i can calculate the order parameter for lipids away from protein as
well. If so please can I know how can i set distance away from protein.
Use index groups specifying different lipids. They are ordered in the
trajectory by distance, so as the molecule number (and thus atom indices)
increase, so too does that molecule's distance from the protein.
-Justin
Kind Regards, chetan
________________________________________ From: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
[jalem...@vt.edu] Sent: 11 October 2011 23:24 To: Discussion list for GROMACS
users Subject: Re: [gmx-users] lipid membrane slicing
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
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jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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