From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Apr 23 2013 - 10:21:03 CDT

Hi Steven,

You'll have to make your own script to do so, and there are many ways of
going about doing it. Just as an example, you could do the following:

mol new 1D1H
set sel1 [atomselect top "index 0"]
set sel2 [atomselect top "index 1"]
for { set i 0 } { $i < [molinfo top get numframes] } { incr i } {
    $sel1 frame $i
    $sel2 frame $i
    puts [vecsub [lindex [$sel2 get {x y z}] 0] [lindex [$sel1 get {x y
z}] 0]]
}

which would print the vector from the atom at index 1 to the atom at
index 0 at every frame in the trajectory loaded by 1D1H.

-Josh Vermaas

On 04/23/2013 06:43 AM, Steven Neumann wrote:
> I want to write a script which makes some calculations based on
> specified vectors. lets presume i want to define a variable which
> describes a specific vector in my protein - e.g. C=O carobxylic group
> vector. What will be the comman to return me this vector at every frame?
>
> Steven
>
>
> On Thu, Apr 18, 2013 at 5:47 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
> <mailto:akohlmey_at_gmail.com>> wrote:
>
> On Thu, Apr 18, 2013 at 5:36 PM, Steven Neumann
> <s.neumann08_at_gmail.com <mailto:s.neumann08_at_gmail.com>> wrote:
> > Dear VMD users,
> >
> > Could you pelase write me how vmd will return you vector of
> specified atom
> > or group of atoms?
>
> huh??
>
> what do you mean by this?
> what context does your question refer to?
> what vectors or groups are you talking about?
>
> axel.
>
>
> >
> > Steven
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
> http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
>