Poojari, Chetan wrote:
Hi Justin,
Using make_ndx on the trajectory file (output from trjorder), and listing out
different lipids i did see the lipids arranged based on the distance from
protein.
Now i want to choose lipids within 0.5nm from protein for my analysis. As in
the index file the lipids are listed based on distance, I am not sure which
lipid numbers fall within 0.5 nm range.
g_select can tell you this.
Please can i know if i can get information about the distance between 1st lipid
listed in index file and the protein, then the 2nd lipid and protein and so on.
Either use g_select or measure distances with g_dist.
-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: 14 October 2011 12:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] lipid membrane slicing
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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Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft:
Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B
3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke
(stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M.
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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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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
--
========================================
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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