I just realized I repeated the script ordering that Thomas already
kindly stated - sorry for that noise!
On Thu, May 18, 2023 at 11:19 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu May 18 2023 - 08:30:03 PDT
