[gmx-users] lipid membrane slicing

[lina]

On Wed, Oct 12, 2011 at 1:20 AM, Poojari, Chetan <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.
>

It seems that the lipid around the protein is not fixed, it's slowly flow
(fluid).

during some time interval, not exactly the same lipids around the protein.
maybe another different group.
so here -sl 2 won't serve well for what you wanna test.



>
>
> Kind Regards,
> chetan
>
>
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