[gmx-users] Lipid Head group Orientation

[Nidhin Thomas]

Hi Chandan,

It would be great if you could share the code with me. 

I had written a similar code in C. But I had considered only P atom and N atom rather than the COM of choline and phosphate groups as mentioned in your paper.

Do you think if there will be a huge difference between these two approaches ?

Thanks a lot!

Nidhin Thomas
PhD Student
University of Houston

> 
> Message: 3
> Date: Fri, 27 May 2016 10:33:29 -0400
> From: Chandan Choudhury <iitdckc at gmail.com>
> To: gmx-users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Lipid Head group Orientation
> Message-ID:
> 	<CAHESojwzBp-pMyX-GHSmHGeBhC16hm3qRaepLYC9KY-h5wBTFw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> 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.
> 
> Chandan
> 
> On Thu, May 26, 2016 at 7:50 PM, Nidhin Thomas <nidhin.thomas0624 at gmail.com>
> wrote:
> 
>> 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
> USA
>