On Wed, May 10, 2023 at 2:33 AM Steinbrecher, Thomas via AMBER
<amber.ambermd.org> wrote:
> outtraj writes immediately. cpptraj commands are not (necessarily) executed
> in the order they are written. This can be confusing indeed.
In my very weak defense, I inherited the syntax from ptraj and decided
backwards compatibility would be the prime directive (except for
'hbond').
> note how trajout is delayed to the end and therefore writes the same
> coordinates as AfterRmsd.crd.
Thomas is correct, 'trajout' happens after all Actions have completed,
so the ordering for the tutorial script is:
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
As far as the original script goes, I would just combine the strip and
align into the same run. If you need a non-aligned and stripped
trajectory, that's where 'outtraj' comes in handy, e.g.:
parm *.prmtop
trajin *.nc
#strip command
strip :WAT,Na+,Cl- outprefix strip
# Write stripped trajectory
outtraj strip.nc netcdf
# align
rms first
# Write aligned trajectory.
# Since it is the last command, can be trajout or outtraj
trajout strip_align.nc netcdf
go
Hope this helps,
-Dan
>
> 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 Thu May 18 2023 - 08:30:03 PDT
