Hi Dulal,
the difference between outtraj and trajout is that one (trajout) waits for
all actions (like rms fitting) to be completed before writing, while
outtraj writes immediately. cpptraj commands are not (necessarily) executed
in the order they are written. This can be confusing indeed. My
understanding is that this is the order of execution in your example
1 trajin mdcrd.crd
5 trajout output.crd
2 outtraj BeforeRmsd.crd
3 rms R1 first :
1-20.CA out rmsd.dat
4 outtraj AfterRmsd.crd
note how trajout is delayed to the end and therefore writes the same
coordinates as AfterRmsd.crd.
Kind Regards,
Thomas
On Wed, May 10, 2023 at 8:21 AM Dulal Mondal via AMBER <amber.ambermd.org>
wrote:
> Dear Users,
>
> I am facing a problem with the difference between trajout and outtraj
> commands.
> I am trying to strip and align my trajectory. For this purpose, I do the
> following steps.
>
> parm *.prmtop
>
> trajin *.nc
>
> #strip command
>
> strip :WAT,Na+,Cl- outprefix strip
>
> trajout strip.nc netcdf
>
> Then I do the following :
>
> parm strip*.promtop
>
> trajin strip.nc
>
> # align
>
> rms first
>
> trajout/outtraj strip_align.nc netcdf
>
> go
> When using the strip command, I use trajin to save strip trajectory.
>
> For saving trajectory after alignment, outtraj command are recommended.
>
> There is a tutorial. https://amberhub.chpc.utah.edu/outtraj/
>
> In this tutorial, It is said that.
>
> trajin mdcrd.crd
> trajout output.crd
> outtraj BeforeRmsd.crd
> rms R1 first :1-20.CA out rmsd.dat
> outtraj AfterRmsd.crd
>
> The output.crd and After-Rmsd.crd trajectories will be identical, but the
> BeforeRmsd.crd trajectory will contain the coordinates of mdcrd.crd before
> they are RMS-fit.
>
> My query is How output.crd and After-Rmsd.crd trajectories are identical?
>
>
>
>
>
>
>
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*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 Wed May 10 2023 - 00:00:02 PDT
