Hi Elisa,
To do what Kenneth is suggesting you, I would recommend to take a look at
the vector command in the cpptraj manual. This would allow you to extract
the component of the distance in a certain direction. You could choose a
reference point like the center of mass of the last atom from your lipids
and evaluate the z-distance component only. A histogram of the distance
measurements should show you the bimodal behavior you are describing.
Hope it helps,
El lun., 9 jul. 2018 a las 19:22, Kenneth Huang (<khuang8.student.gsu.edu>)
escribió:
> Hi,
>
>
> You could try to use measuring the distance in cpptraj if you know a fixed
> reference point that you can measure the aspartate distance to and see how
> it changes with time.
>
>
> You could also look at the waters around it, ie watershell, if your
> residue is becoming buried in the membrane, but that might be trickier to
> interpret if there happens to be enough water around in both positions.
>
>
> Best,
>
>
> Kenneth
>
> ________________________________
> From: Elisa Pieri <elisa.pieri90.gmail.com>
> Sent: Monday, July 9, 2018 9:12 AM
> To: AMBER Mailing List
> Subject: [AMBER] Help on
>
> Hello everyone,
>
> I'm running a simulation of a protein in membrane (explicit solvent). I
> have a ASP residue that is located at the frontier between water and
> membrane, and it is dynamically flipping from being embedded in the
> membrane and facing the water. I would like to plot this property against
> the time coordinate. Since I have no MM analysis background on this topic,
> could you tell me what kind of analysis should/could I run (presumably with
> cpptraj)?
>
> Sorry for this trivial question..could you help me?
>
> Elisa
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Ckhuang8%40student.gsu.edu%7Cebaae0cbae8143e5d9af08d5e59db29a%7C704d822c358a47849a1649e20b75f941%7C0%7C0%7C636667387823752021&sdata=Yr%2FN2qg5XDzwjVEO4KcC2OYB%2Bk3kEtbZ63WoDJHNjMo%3D&reserved=0
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Stephan Schott Verdugo
> Biochemist
>
> Heinrich-Heine-Universitaet Duesseldorf
> Institut fuer Pharm. und Med. Chemie
> Universitaetsstr. 1
> 40225 Duesseldorf
> Germany
>
> <http://lists.ambermd.org/mailman/listinfo/amber>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 09 2018 - 11:00:01 PDT
