Oops ... I forgot to mention that you'll have to do a little
post processing to get what you want. If you do ...
trajin mdcrd.1
trajin mdcrd.2
rms2d ... blah ... blah ... args
... you'll get the "intra-rmsd" data as well as the "inter-rmsd".
So if you plot the whole thing, you can cut out just the "square"
of the plot that you want (rmsd between mdcrd.1 vs mdcrd.2).
Or you could make a post-processing script to pull out the data
that you want.
--Niel
________________________________________
From: Niel Henriksen [niel.henriksen.utah.edu]
Sent: Tuesday, May 28, 2013 6:59 AM
To: AMBER Mailing List
Subject: Re: [AMBER] RMSD calculation between trajectories
Hi Dilraj,
Check out the "rms2d" analysis command in cpptraj (AmberTools13).
Previous versions of cpptraj and ptraj also support it, but I'm not sure
if it was documented.
--Niel
________________________________________
From: dilrajl.bii.a-star.edu.sg [dilrajl.bii.a-star.edu.sg]
Sent: Tuesday, May 28, 2013 6:42 AM
To: amber.ambermd.org
Subject: [AMBER] RMSD calculation between trajectories
Dear Amber Users,
I have two separate trajectories and I want to
compute the RMSD between each frame of the first trajectory with every
frame of the second trajectory.
Is there any means by which one can do this in ptraj or cpptraj?
Or if someone has tried this before, could you please direct in
performing this analysis.
Thank you.
Dilraj.
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Received on Tue May 28 2013 - 06:30:02 PDT
