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>
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Received on Mon Jun 25 2018 - 05:00:01 PDT
