AMBER Archive (2000)

Subject: Re: HEllo!

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Sep 29 2000 - 14:57:22 CDT

        I was just wondering if anyobe can tell me how to FIT the RMSD of the
        coordinate set (i+1) to the coordinate set (i) in CARNAL? In the other
        word, I have a trajectory contained many snapshots and I want to compute
        the RMSD of the snapshot (i+1) against the snapshot (i) rather than
        compute the RMSD of snapshot (i+1) against the first snapshot or the one
        defined as STATIC. Thanks for your help!
        
You can do the triangular matrix of all coordinate sets, i.e.

  i=1..n-1: { i:i+1, i:i+2 .. i:n }

if you use a STATIC instead of STREAM for your coordinate set.
Beyond that, a new feature would have to be added.

Bill Ross