Hi Chen,
it sounds like half of what you want is built into cpptraj, you can create
multiple coordinate sets out of your trajectory with the createcrd command
without writing to disk again. The one thing I didn't find, where someone
with more cpptraj experience may need to comment, is a good way to strip
individual frames out of a crdset using the onlyframes notation.
Kind Regards,
Thomas
On Tue, Feb 21, 2023 at 1:16 PM XP Chen via AMBER <amber.ambermd.org> wrote:
> I want to do some analysis (here is `watershell`) on some specific frames.
>
> I use a not-easy way as follows. However, it will create new trajectory
> files, and make it not convenient for large trajectories. Is there any
> elegant way to do analysis on specific frames which do not fulfill `<start>
> <stop> <offset>` in `trajin`?
>
> 1. First split the trajectory
> ```
> parm A.prmtop
> trajin A.nc
>
> trajout B1.nc netcdf onlyframes 1,78,100,101,170
> trajout B2.nc netcdf onlyframes 8,82,88,99,120,125
> run
> ```
>
> 2. Then reload the new trajectory and do the analysis
> ```
> parm A.prmtop
> trajin B1.nc
>
> watershell :5.SG out wa.out lower 3.5 upper 5.0 :WAT
> run
> ``
>
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>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Tue Feb 21 2023 - 05:30:02 PST
