AW: Movie of a channel trajectory

From: Norman Geist (
Date: Mon Apr 07 2014 - 02:05:25 CDT

You could try:

1. Use pbc wrap with centering of your channel, so it will stay on the same
location. This will only "move" your system within X,Y,Z. Command like: pbc
wrap -all -compound res -center com -centersel "your channel selection"

2. Use the RMSD Trajectory Tool to align you channel, so it will stay on the
same location. This will brake pbc as system is also rotated.

3. For the representation of your channel surface, choose under the
trajectory tab for "Draw multiple Frames" not "now" but any frame number you
want the channel to stay at. This is only a good choice if your channel
doesn't move much. You might need to do one of the above steps before
anyway, so that the water is actually there were you visualize the channel.

Best option might be the 1+3.

PS: This is a VMD question.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Javier Cáceres Delpiano
> Gesendet: Sonntag, 6. April 2014 05:26
> An:
> Betreff: namd-l: Movie of a channel trajectory
> Hello,
> I want to make a movie of a trajectory, similar to the movie attached
> to files in the case study of aquaporins.
> The idea is to cut in half my protein to see the channel surface and
> see solute transport, but I don’t want the surface of my channel move,
> only the waters. Any help?
> Please!
> I attached the link in case you want to see the movie.
> Thanks!

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