From: Johannes Müllegger (hannes_at_zymeworks.com)
Date: Wed Aug 23 2006 - 19:25:58 CDT

Dear VMD users,

        I am observing strange spikes in my rmsd calculations on
trajectories using the 'RMSD Trajectory Tool' (VMD 1.8.4 on Gentoo
Linux). The spikes seem to appear at different timepoints and only
one of the frames at a time is affected. I have aligned the frames
with either the function that is included in the RMSD Trajectory plug
in (Reference molecule top, protein and noh) or with a script that I
wrote (using the selection [atomselect top all]) with the same
outcome. When I redo the alignment the spikes disappear. The height
of the spikes is about 0.1 to 0.3 above the other values which are ~1
and there are from 1 to 4 of these spikes in a trajectory of 4000
frames.
Has anybody observed similar behavior or is that a specific problem
of my trajectory files? Anything I can do to avoid that?

Thanks for your help
-hannes-

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Johannes Müllegger
Enzyme Engineer
Zymeworks Inc.
201 - 1401 West Broadway
Vancouver, BC, Canada
V6H 1H6
Phone: 604 678 1388 -29
Fax: 604 737 7077
www.zymeworks.com

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