[gmx-users] lipid membrane slicing

Poojari, Chetan c.poojari at fz-juelich.de
Wed Oct 19 20:23:41 CEST 2011 

Hi Justin,

I used the below g_select command to get the list of phosphorus atoms (from DPPC lipid) within 0.5 nm of protein. 

g_select -f ordered.xtc -n initial.ndx -on select.ndx -select "name P and within 0.5 of group Protein" -s md_500ns.tpr -b 100000 -dt 1000

My output is an index file which contains different phosphorus atom number at each frame within 0.5nm of protein and this number changes for every frame.

Please can I know if its possible to use this index file to convert each frame into trajectory file and do analysis for lipids within 0.5 of 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: 17 October 2011 20:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] lipid membrane slicing

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-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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>> -- ========================================
>>
>> 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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>

--
========================================

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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