Hi,
The rms2d command in cpptraj has a 'reftraj' option that will do what
you want. So say you have two trajectories, traj1.nc and traj2.nc,
both have the same topology, and you want RMSD based on C-alpha atoms;
your cpptraj input may look like:
parm prmtop
trajin traj1.nc
rms2d out output.dat reftraj traj2.nc .CA
Note that if you want gnuplot-compatible output change the output file
name extension to .gnu (e.g. output.gnu).
Hope this helps,
-Dan
On Tue, May 28, 2013 at 6:42 AM, <dilrajl.bii.a-star.edu.sg> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue May 28 2013 - 07:30:03 PDT
