[gmx-users] Lipid Head group Orientation

Chandan Choudhury iitdckc at gmail.com
Fri May 27 16:33:52 CEST 2016

Hi Nidhin!

I wrote a code some time ago on the the orientation of lipid molecules
which was the specific to the problem addressed at
http://pubs.acs.org/doi/full/10.1021/bm4011408. If you need, I can share.


On Thu, May 26, 2016 at 7:50 PM, Nidhin Thomas <nidhin.thomas0624 at gmail.com>

> Hi GROMACS Users,
> This question was asked before in the forum. But I could not find a
> complete answer. So I’m asking again. Is there any command in GROMACS that
> can give the orientation of lipid head groups of all lipids averaged over
> time?
> I wrote a code which takes the co-ordinates of P and N atoms at each time
> frames and gives the orientation of P-N vector averaged over the time. I
> was wondering if there is any command in GROMACS that can provide this data
> directly ?
> I used g_sgangle command to obtain the angles of one lipid molecule. But
> how do we get the data for all lipids in one file?
> Thanks,
> Nidhin Thomas
> University of Houston
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Chandan Kumar Choudhury
Post Doctoral Fellow
Clemson University
South Carolina

*"All work and no play makes Jack a dull boy...”*

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