VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 16 2010 - 13:01:21 CDT
- Next message: Michael LeVine: "Invalid command name "His" during Solvation"
- Previous message: Ardy Davari: "Color by velocity (speed?)"
- In reply to: Ardy Davari: "Color by velocity (speed?)"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
On Wed, Jun 16, 2010 at 1:04 PM, Ardy Davari <ardydavari_at_gmail.com> wrote:
> Hi,
>
> Is it possible to color by speed of an atom using a charmm35 psf and dcd
> file? I came across the post attached below, and I am not sure how to do
> this in 1.8.7.
have you actually tried it? VMD hasn't changed in
that respect since john posted the message.
just create a script that loops over all frames,
computes the velocity and then stores it in a
user field and color by user. bingo!
cheers,
axel.
>
> Best Regards,
>
> Ardy Davarifar
>
> ****Attached post ***
>
> Hi,
> One can do that in the test versions of VMD 1.8.7 now, with a script,
> by querying the atom velocity components and drawing an arrow for each
> of the atoms of interest. The new velocity component keywords are
> "vx", "vy", and "vz". You can do something like:
> set sel [atomselect top "index 1 to 5"]
> set coords [$sel get { x y z }]
> set velocities [$sel get { vx vy vz }]
> ...normalize the velocities to some scale...
> ...draw the arrow from the coordinate to an endpoint calculated by
> adding the scaled velocity vector to the coordinate...
>
> See Axel's tutorial on various customized drawing commands,
> and dynamically updating graphics:
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect1
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect2
>
> You can also color by velocity in the new alpha versions of VMD 1.8.7.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
- Next message: Michael LeVine: "Invalid command name "His" during Solvation"
- Previous message: Ardy Davari: "Color by velocity (speed?)"
- In reply to: Ardy Davari: "Color by velocity (speed?)"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]