AMBER Archive (2005)

Subject: Re: AMBER: comparing md trajectories

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Tue Jul 19 2005 - 07:58:44 CDT

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

ayongye_at_chem.uga.edu 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
>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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