Hi Christopher,
Actually I made a mistake! Sorry for that. It should be "center :1-192 mass
origin", the image command is not even necessary. The small difference you
see there is because the centering was made with the geometrical center,
not the COM; the result should be a 0 drift. Just remember to unwrap if you
used iwrap = 1 during the MD run.
Cheers,
El lun., 25 jun. 2018 a las 13:41, Christopher Faulkner (<
FaulknerC3.cardiff.ac.uk>) escribió:
> Hi Stephan,
>
>
> Thank you for your reply. Before using your suggestion the output I
> received from the command:
>
>
> trajin bilayer_run.nc
>
> vector com center out upper_movement.dat :1-192
>
> run
>
>
> was (only first 10 frames shown):
>
>
> #Frame com
> 1 37.9651 38.1393 50.0894 0.0000 0.0000 0.0000
> 2 36.9363 36.9393 48.9798 0.0000 0.0000 0.0000
> 3 35.8655 35.7601 47.6255 0.0000 0.0000 0.0000
> 4 34.5760 34.6131 46.3186 0.0000 0.0000 0.0000
> 5 33.8026 34.2025 45.4674 0.0000 0.0000 0.0000
> 6 33.4618 33.8888 45.0800 0.0000 0.0000 0.0000
> 7 33.1437 33.8499 45.0493 0.0000 0.0000 0.0000
> 8 33.0836 33.9396 44.8722 0.0000 0.0000 0.0000
> 9 33.0088 33.9056 44.7565 0.0000 0.0000 0.0000
> 10 32.8779 34.0202 44.7035 0.0000 0.0000 0.0000
>
>
> If I use your suggested command (center :1-192 origin image origin) and
> re run the vector command I receive the output:
>
>
> #Frame com
>
> 1 0.0316 -0.0490 1.1963 0.0000 0.0000 0.0000
>
> 2 -0.0012 -0.0772 1.1740 0.0000 0.0000 0.0000
>
> 3 -0.0166 -0.0669 1.1415 0.0000 0.0000 0.0000
>
> 4 1.1073 1.0055 1.1384 0.0000 0.0000 0.0000
>
> 5 -0.0569 1.0073 1.1404 0.0000 0.0000 0.0000
>
> 6 0.9830 0.9686 1.1450 0.0000 0.0000 0.0000
>
> 7 0.9609 -0.0627 1.1429 0.0000 0.0000 0.0000
>
> 8 -0.1265 -0.0893 1.1236 0.0000 0.0000 0.0000
>
> 9 -0.1086 0.9531 1.1288 0.0000 0.0000 0.0000
>
> 10 -0.1553 0.9610 1.1247 0.0000 0.0000 0.0000
>
>
> Does this correspond to the COM drift? And if so how do I reset the
> monolayer by the corresponding movement
>
> (in X, Y, Z) to create a new trajectory without monolayer COM drift so I
> can calculate the lateral diffusion?
>
>
> Regards,
>
> Christopher
>
> ________________________________
> From: Stephan Schott <schottve.hhu.de>
> Sent: 22 June 2018 11:44:42
> To: AMBER Mailing List
> Subject: Re: [AMBER] Lipid diffusion COM drift
>
> Hi Christopher,
> You can try with something like this before running your analysis:
>
> center :1-192 origin
> image origin
>
> If you have wrapping turned on, make sure to unwrap the trajectory first,
> or this will not work properly. You can recheck the COM with the vector
> command.
> Let me know if it works.
> Cheers,
>
> El vie., 22 jun. 2018 a las 10:45, Christopher Faulkner (<
> FaulknerC3.cardiff.ac.uk>) escribió:
>
> > Dear Amber users,
> >
> >
> > I am having some trouble in the correction of COM drift in my lipid
> system
> > so I can calculate diffusion coefficients.
> >
> >
> > I have found the movement of the upper monolayer COM using the cpptraj
> > commands:
> >
> >
> > trajin bilayer_run.nc
> >
> > vector com center out upper_movement.dat :1-192
> >
> > run
> >
> >
> > I have created the new prmtop and trajectory of the upper monolayer only:
> >
> > parm DOPC.prmtop
> > trajin DOPC.nc
> > strip !(:1-192) outprefix upper
> >
> > trajout DOPCupper.nc
> > run
> >
> >
> > I am unsure about how to reset the monolayer by the corresponding
> movement
> > (in X, Y, Z) to create a new trajectory without monolayer COM drift.
> >
> >
> > Any help is appreciated,
> >
> >
> > Christopher Faulkner
> >
> > PhD student
> >
> > Cardiff University
> > _______________________________________________
> > 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
> _______________________________________________
> 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>
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Received on Mon Jun 25 2018 - 06:30:03 PDT
