[AMBER] trajin and outtraj command

From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Wed, 10 May 2023 11:50:58 +0530

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.*
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Received on Tue May 09 2023 - 23:30:02 PDT
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