VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 26 2014 - 23:58:13 CST
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Hi,
The 'measure' routines are all C/C++.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Wed, Nov 26, 2014 at 09:55:47PM -0800, Gianluca Interlandi wrote:
> Hi John,
>
> Thanks a lot for the detailed explanation. Just curiosity, are the measure
> routines of VMD coded in TCL or in C? I guess C, but just checking.
>
> Thanks!
>
> Gianluca
>
> On Wed, 26 Nov 2014, John Stone wrote:
>
> >Hi,
> > A few points. DCD files store coordinates in single precision only,
> >not double precision. Restart files are often double precision,
> >but most trajectory formats are only single precision. The various
> >"measure" routines in VMD are dominated by single precision since that's
> >how VMD also stores atomic coordinates associated with trajectory
> >frames currently. Tcl math routines are mostly double precision,
> >so there will be differences in rounding, vector length normalization,
> >etc if you invoke routines that are doing math in the more conventional
> >Tcl way. In any case, since your atomic coordinates in VMD are currently
> >only stored in single precision, that's all you should expect from
> >most distance measurements and the like. Since floating point is
> >non-associative, any change in the order of operations (even a tiny one)
> >can cause the results of two otherwise comparable calculations to differ,
> >so your results are exactly what I would expect to see.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Wed, Nov 26, 2014 at 04:06:03PM -0800, Gianluca Interlandi wrote:
> >>Dear vmd list,
> >>
> >>I noticed that I get slightly different results when I measure the
> >>distance between two atoms using "measure bond" vs by measuring the length
> >>of the vector between the two atoms. The difference is usually after the
> >>4th decimal after the period. I read in the frames from a NAMD DCD and I
> >>use, e.g.,:
> >>
> >>set index1 [[atomselect top "name CA and resid 1"] get index]
> >>set index2 [[atomselect top "name CA and resid 2"] get index]
> >>measure bond {$index1 $index2} frame 100
> >>
> >>which returns "12.263489723205566"
> >>
> >>But if I calculate the length of the vector between the two atoms with:
> >>
> >>set sel1 [atomselect top "name CA and resid 1" frame 100]
> >>set sel2 [atomselect top "name CA and resid 2" frame 100]
> >>set res1 [lindex [$sel1 get {x y z}] 0]
> >>set res2 [lindex [$sel2 get {x y z}] 0]
> >>veclength [vecsub $res2 $res1]
> >>
> >>I get "12.26349001762006"
> >>
> >>Just wondering how come I get two slightly different results? The frames
> >>are read from a DCD file that should be double precision. Which of the two
> >>methods should be in theory more precise?
> >>
> >>Thanks!
> >>
> >> Gianluca
> >>
> >>-----------------------------------------------------
> >>Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> >> +1 (206) 685 4435
> >> http://artemide.bioeng.washington.edu/
> >>
> >>Research Assistant Professor at the Department of Bioengineering
> >>at the University of Washington, Seattle WA U.S.A.
> >>-----------------------------------------------------
> >
> >--
> >NIH Center for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> >http://www.ks.uiuc.edu/Research/vmd/
> >
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Assistant Professor at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/
- Next message: Norman Geist: "AW: Re: Need testers: VMD 1.9.2 w/ interactive GPU ray tracing w/ AO, depth of field, etc."
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- In reply to: Gianluca Interlandi: "Re: "measure bond" vs veclength"
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