On Wed, 16 Mar 2016 11:47:52 +0000
Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
> trajin md_simulation_combine.nc
> rms first :1-532.CA,C,N out rmsd.dat
> strip :WATER
> strip :Na+
You are reading a single trajectory file here. How many frames does it
contain, how have you created this file? Check this first.
As far as cpptraj is concerned there is no need to combine trajectories
beforehand. I would recommend to use multiple "trajin" commands to
read in the original files.
The rms command has an option "time" which you can use to scale the
x-axis to your liking. See the manual. If you do not use "time" then
the x-axis is simply the number of frames. So why does the file
md_simulation_combine.nc have so many? You originally indicated there
should be only half that number.
The final "strip" commands don't seem to do anything useful here (unless
your script is longer and you do something else with the stripped
topology later). I suspect that the ":WATER" mask should actually
be ":WAT".
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Received on Wed Mar 16 2016 - 05:30:03 PDT
