AMBER Archive (2005)

Subject: AMBER: comparing md trajectories

From: ayongye_at_chem.uga.edu
Date: Mon Jul 18 2005 - 20:12:15 CDT

Dear amber users,
I have two separate MD trajectories (T1 and T2) of the same compound in
different starting conformations. I am analysing the trajectories in order
to find out whether they converge to the same structure as the simulation
proceeds.
I have used carnal, but it computes the rmsds between sequential frames in
both trajectories.
Can someone let me know how to generate a 2d-rmsd plot of the two
trajectories, with T1 on the x-axis and T2 on the y-axis ie compare each
frame in T1 with every frame in T2?
Thanks,
Austin B. Yongye

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