[gmx-users] lipid membrane slicing

[Justin A. Lemkul]

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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-- 
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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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