VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 16 2008 - 15:43:17 CDT

Hi,
  We've already changed the RMS fit code in VMD since VMD 1.8.5
and tightened the tolerances, but I'll have a look at your patch
and compare with the current implementation, as well as passing it
along to the NAMD developers.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Oct 11, 2008 at 04:05:45PM -0400, Stephen Hicks wrote:
> Hi,
>
> I have a VMD script that automatically performs a huge number of
> 'measure fit's, and I would occasionally notice that it would just
> leave out the rotational part and simply return the identity matrix
> with a translation. I was wondering where this came from and I
> tracked it down to the fact that the Jacobi diagonalization is
> quitting prematurely in fitrms.c. It uses a pretty standard algorithm
> - rotating the matrix along each of the three axes in turn, but it
> stops the moment rotation about a single axis doesn't improve the fit
> by more than tol, which is set rather large. To fix it, I require
> that all three axes show no improvement AND I decrease tol by a whole
> lot. Since Jacobi's method converges quadratically, this shouldn't
> cause any problems.
>
> I've uploaded an example of the bug and a patch for fixing it. A
> similar patch should also be applied to NAMD, since the same algorithm
> is used there (in fitrms.C), although the smaller tol might break if
> it's compiled with floats instead of doubles, so that might need to be
> tailored.
>
> The files are available at http://tinyurl.com/47ta8b
>
> steve hicks 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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