[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 111

[Nidhin Thomas]

Hi Tom,

Thanks a lot for your input.

Cheers!

Nidhin Thomas

> Message: 7
> Date: Sat, 28 May 2016 00:39:29 +0100
> From: Thomas Piggot <t.piggot at soton.ac.uk>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Lipid Head group Orientation
> Message-ID: <5748DAB1.5000901 at soton.ac.uk>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> 
> 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
>>>> --
>>>> Gromacs Users mailing list
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>>> 
>>> 
>>> 
>>> -- 
>>> 
>>> Chandan Kumar Choudhury
>>> Post Doctoral Fellow
>>> Clemson University
>>> South Carolina
>>> USA
>>> 
> 
> -- 
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.