vmd-l: boubt about consistency of measures

From: Sergio Anis (sergioanis_at_ispwest.com)
Date: Thu Mar 23 2006 - 08:19:52 CST

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


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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