VMD-L Mailing List

From: Justin Gullingsrud (jgulling_at_mccammon.ucsd.edu)
Date: Fri Jun 11 2004 - 10:07:54 CDT

Hi,

Yes, this is a recently corrected bug in the fitting algorithm,
affecting VMD 1.8.2. There should be beta versions of VMD available
upon request that do not have this problem.

As a workaround, I think you can avoid the bug by moving the reference
system so that it's center is at the origin. Best of course would be
to use a newer VMD version.

Cheers,
Justin

On Jun 11, 2004, at 12:48 AM, Jérôme Hénin wrote:

> Hi all,
>
> I have met an unexpected behaviour using the "measure fit" command,
> and I'd
> like to know if anyone has had a similar experience.
>
> When computing the rmsd along a trajectory, some frames were not
> properly
> aligned with the reference system, which resulted in jumps in the
> measured
> rmsd. By repeating the fitting procedure, the alignement problem was
> eventually corrected.
>
> Is this to be considered a bug of the alignement algorithm?
>
> Jerome
> 

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