From: John Stone (
Date: Wed Aug 23 2006 - 22:27:52 CDT

  Is the behavior you're observing deterministic, or is it random?
If you load the same trajectory and perform the same sequence of
RMSD and alignment operations in two successive VMD sessions, do
you get precisely the same results? I've just recently run the Linux
version of VMD through valgrind while running Luis' RMSDTT plugin
to measure RMSD and align trajectory frames, and didn't see any
signs of problems, nor did I see such spikes in my testing. Which
version of VMD are you using, the 32-bit or 64-bit build?
Depending on whether the behavior you're seeing is deterministic or
random, I may have some further experiments for you to try on your machine.

  John Stone

On Wed, Aug 23, 2006 at 05:25:58PM -0700, Johannes Müllegger wrote:
> 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-
> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
> Johannes Müllegger
> Enzyme Engineer
> Zymeworks Inc.
> 201 - 1401 West Broadway
> Vancouver, BC, Canada
> V6H 1H6
> Phone: 604 678 1388 -29
> Fax: 604 737 7077
> _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

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