VMD-L Mailing List
From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Apr 23 2013 - 10:21:03 CDT
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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.
>
>
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