Re: vmd-l: boubt about consistency of measures

From: John Stone (
Date: Mon Mar 27 2006 - 00:47:16 CST

Hi Sergio,
  Just to eliminate possible sources of confusion, did you compare
these inter-atom distances with and without the RMS best fit matrix
being applied? (i.e. comment out the '$all move [measure fit ....]' line
and see if you get distances that are significantly different from those
you get when the fit is applied. Since what you're concerned about is
the effect of the RMS fit matrix transformation, let's make absolutely sure
you're comparing against exactly the same per-frame distances. Try running
that with the RMS fit transformation removed and see how they compare.
If you do see an unusually large change in distance between the transformed
per-frame coordinates and the original per-frame coordinates, then we'll have
to look into this deeper.

  John Stone

On Thu, Mar 23, 2006 at 06:19:52AM -0800, Sergio Anis wrote:
> hi everybody;
> I have a doubt about the consistency of the rmsd and distances between atoms measurements.
> The situation is the following:
> * I have a simulation and computed the rmsd (using the script provided with the tutorial) and, without closing vmd, measured the distances beetwen atoms (using label->bonds->save)
> * I had to make an extended simulation and since it doesn't fit in my ram I modified the bigdcd script to do all the measurements
> To test the script I used it on the first simulation and compare the results. I found that the rmsd are differents (they are quite similars, this is not surprising since the matrix transformation is not the same every time). What did surprise me is the differences in the distances (in some cases is about 2A)
> So, my question are how reliable are these measures and if the matrix transformation can change the distances between atoms?
> Below you can see the script I used.
> I'd really appreciate your thoughts
> best
> Sergio
> proc myproc { frame } {
> set outfile [open data.txt a+];
> global ref sel all atom1 atom2 atom3 atom4 atom5 atom6 atom7
> $all move [measure fit $sel $ref]
> set pos1 [$atom1 get {x y z}]
> set pos2 [$atom2 get {x y z}]
> set pos3 [$atom3 get {x y z}]
> set pos4 [$atom4 get {x y z}]
> set pos5 [$atom5 get {x y z}]
> set pos6 [$atom6 get {x y z}]
> set pos7 [$atom7 get {x y z}]
> set dist1 [vecdist [join $pos1] [join $pos2]]
> set dist2 [vecdist [join $pos3] [join $pos4]]
> set dist3 [vecdist [join $pos3] [join $pos5]]
> set dist4 [vecdist [join $pos6] [join $pos7]]
> puts $outfile "$frame: [measure rmsd $sel $ref] $dist1 $dist2 $dist3 $dist4"
> close $outfile
> }
> package require bigdcd
> mol load psf 1cp4_w.psf
> set all [atomselect top all]
> set ref [atomselect top "name CA" frame 0]
> set sel [atomselect top "name CA"]
> set atom1 [atomselect top "index 3840"]
> set atom2 [atomselect top "index 1572"]
> set atom3 [atomselect top "index 1005"]
> set atom4 [atomselect top "index 2326"]
> set atom5 [atomselect top "index 3681"]
> set atom6 [atomselect top "index 3780"]
> set atom7 [atomselect top "index 1417"]
> animate read dcd 1cp4_eq.dcd beg 0 end 0 # set the first frame as reference for rmsd
> bigdcd myproc 1cp4_eq.dcd

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