[gmx-users] lipid membrane slicing

[Poojari, Chetan]

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.


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.



Kind Regards,
chetan


________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at 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.poojari at fz-juelich.de <mailto:c.poojari at 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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