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
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>
> --
> 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 Fri Jun 22 2018 - 04:00:02 PDT
