[gmx-users] lipid membrane slicing

Mon Oct 17 20:23:14 CEST 2011

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.

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.

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: 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-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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>>  Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft:
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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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--
========================================

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
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