[gmx-users] Lipid Head group Orientation

[Thomas Piggot]

Hi Nidhin,

If, as you previously mentioned, you want to use a GROMACS tool for this 
type of analysis, you can write a fairly trivial shell script to loop 
over g_sgangle for all of the individual lipids within your membrane and 
then you can combine all the outputs together using something like 
xmgrace. This is what I've done in the past. One word of advice is that 
just need to make sure you are measuring the same angle when looking at 
both leaflets of the membrane.

Cheers

Tom

On 27/05/16 17:10, Nidhin Thomas wrote:
> 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
>>

-- 
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.