VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Aug 07 2010 - 20:42:05 CDT

On Sat, Aug 7, 2010 at 8:51 PM, Marc Zimmer <mzim_at_conncoll.edu> wrote:
> Hi

hi marc,

> We have a trajectory of  our protein in a box of waters and would like to
> superimpose the protein and plot the position of a specific water molecule
> in each frame, so that we can get an average protein structure (or a
> representative protein structure) with position of the water molecule in all
> the frames superimposed on that single protein structure  showing the
> pathway that water takes out of the protein.

just create two visualizations: one for the protein and one for the water.
for the water you go to the Trajectory tab and have a look at the
"Draw Multiple Frames" option. here you have the option to superimpose
multiple frames between frames "b" and "e" and optionally showing only
every "s"th frame. for more details, see the user's guide.

an alternate way to show the path of a selected group of
atoms is this script:

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/trajectory_path/

cheers,
    axel.

>
>
> Any suggestions or scripts would greatly be appreciated.
>
> Thanks a lot
>
> Marc Zimmer 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.