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
