Re: AMBER: comparing md trajectories

From: Carlos Simmerling <>
Date: Tue, 19 Jul 2005 08:58:44 -0400

moil-view can do this (it is on the Amber CD but requires
an SGI computer to run). ptraj might do it, check the manual.
carlos wrote:

>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
>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?
>Austin B. Yongye
>The AMBER Mail Reflector
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Received on Tue Jul 19 2005 - 14:53:01 PDT
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