[gmx-users] Lipid tilts
X.Periole at rug.nl
Fri Jan 14 08:40:40 CET 2005
On Thu, 13 Jan 2005 14:28:55 +0000
Qing Zhu <qing.zhu at ttu.edu> wrote:
> Hi, everyone:
> I just finished a MD simulation of lipid membrane
>system, and I am
> trying to get the lipid tilts relative to membrane
>normal. In gromacs I only found the program g_bundle can
>do such kind of stuff, but the results from g_bundle are
>pretty weird (maybe the method I used was wrong). So I
>just want to know is there a good program or method in
>gromacs which can be used to get the lipid tilts relative
>to membrane normal? Any suggestion will be appreciated !
For lipids the tilt angle relative to the normal is not
really meaning full as the lipid is composed by different
parts: basicaly one head group and two tails for the most
commonly used lipids. So you'd have to play with a subset
of atoms to get a meaningfull information.
It could be more interesting for you to use the order
parameter(g_order), which gives the order of the chain
relative to the position of the carbon atom in the acyl
chain. This is assuming that you are interesting in the
orientation of the lipids in your bilayer.
Note also that depending on the nature of the lipid you
simulate it could be that the lipid tails have different
tilt depending on the part of the tail.
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