[gmx-users] lipid membrane slicing

Igor Marques igor.dragon88 at gmail.com
Tue Oct 11 22:28:56 CEST 2011


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.

good luck,

      Igor Marques

On Tue, Oct 11, 2011 at 6:20 PM, 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.
> Kind Regards,
> chetan
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