VMD-L Mailing List

From: Justin Gullingsrud (jgulling_at_mccammon.ucsd.edu)
Date: Thu Feb 19 2004 - 12:45:52 CST

Juan,

If speed is an issue in your analysis scripts and VMD's single-precision
vector operations aren't sufficient, you might want to consider writing
your analysis script in C and using SWIG (www.swig.org) to generate a
Tcl interface.

Cheers,
Justin

On Mon, Feb 16, 2004 at 11:56:13PM -0600, John Stone wrote:
>
> Juan,
> I believe the cause of misunderstanding here is that
> the implementation of veclength in VMD is done in single
> precision, and so that's precisely the reason you're getting
> a weird answer. The implementation in VMD is not using all of
> the digits of the two constants in your example below, they are
> being truncated to single-precision, and thus the answer is a
> smaller number than the original double-precision numbers.
> (keep in mind that the square of that second number is quite small..)
>
> So, the answer is correct given that the implementation is all
> single-precision floating point arithmetic (all the way through
> including the squaring, summation, and square root call...)
> That's also why its faster than doing it various other ways.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Feb 16, 2004 at 07:54:55PM -0800, Juan Alfredo Freites wrote:
> > Dear John and VMD users,
> >
> > In some instances veclegth isn't giving me the right answer, here is an
> > example
> >
> > veclength {2.37137085199 0.000350952148438}
> > 2.37137079239
> >
> > we can see that is wrong because the answer is less than one the
> > components, conventional expr{} gives the right answer
> >
> > expr
> > {sqrt((2.37137085199*2.37137085199)+(0.000350952148438*0.000350952148438))}
> > 2.37137087796
> >
> > but it's twice more expensive than veclength. I also tried veclength [list
> > ...] so as to avoid any ambiguity, but got the same result.
> >
> > any thoughts?
> >
> > --
> > J. Alfredo Freites
> > Department of Physics
> > University of California, Irvine
> > Irvine, CA 92697-4575
> > (949) 824-9921
> >
>
> --
> 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
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078