VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Feb 09 2007 - 07:57:09 CST

Sure you can; the best way is to load them as two separate molecules,
and then map the forces from one file onto the user field of the other
(since the user field can store time-variant data for atoms). So
assuming you have the files

coords.xyz -- coordinates of interest
forces.xyz -- xyz file with forces

and they have the same number of atoms and such, you could do the following:

set allsel [atomselect 0 all] ;# assuming mol 0 is coords
set forcesel [atomselect 1 all]

for {set i 0} {$i < [molinfo get numframes]} {incr i} {
    $forcesel frame $i

    foreach atomind [$allsel get index] force [$forcesel get {x y z}] {
        set csel [atomselect 0 "index $index" frame $i]
        set forcemag [veclength $force]
        $csel set beta $forcemag
        $csel delete
    }
}

$allsel delete
$forcesel delete

You can then get the picture you want by coloring the atoms by the user
field, making sure you have "update color every frame" checked in the
trajectory tab of the graphical representations menu.

Peter

Adrian Koh wrote:
> Hi,
>
> I know this been asked countless of times, but I couldn't seem to get
> the gist of it. I have a .xyz trajectory file (containing the
> positions of atoms for every frame, 250 frames in all). And I have
> another .xyz file (containing the atomic resultant forces on every
> atom, for the 250 frames). Would I be able to combine the two files,
> request VMD to plot the positions of the atoms with the corresponding
> color codes based on the magnitude of the atomic resultant force, all
> in one single animation?
>
> How do I do it?
>
> Thanks!
>
>
> Best Regards,
> Adrian.
>
>