From: Jim Kress (jimkress_58_at_kressworks.org)
Date: Thu May 24 2012 - 13:38:23 CDT

Hi Axel,

Here's my procedure:

1. From VMD Main Load gromacs trajectory into VMD
2. From VMD Main Load associated .gro file data into VMD
3. from VMD Main Do: graphics > representations > trajectory and then set
trajectory smoothing window size to 10
4. Go back to VMD Main and do play forward to check the trajectory playback.
Speed is at highest setting.
5. From VMD Main stop the playback and set slider back to "0" position
6. From VMD Main do: extensions > visualization > movie maker and movie
maker Tk applet pops up
7. Set working directory
8. Name movie
9. Set rotation angle to 0
10. leave trajectory step size set at 1 (the default when the applet pops
up)
11. leave the renderer at default (snapshot)
12. do Movie Settings > Trajectory
13. leave Format as MPEG 1
14. click on Make Movie

Now it works OK. I think it was not working properly because; previously I
had set the step size at 10 in movie maker. That seems to have confused the
VMD/ Movie Maker link. If I don't mess with the defaults, all is OK.

As usual, thanks for your help!

Jim

> -----Original Message-----
> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> Sent: Thursday, May 24, 2012 1:03 PM
> To: Jim Kress
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Movie making with smoothed trajectories
>
> On Thu, May 24, 2012 at 12:02 PM, Jim Kress <jimkress_58_at_kressworks.org>
> wrote:
> > I have a 7500 frame gromacs trajectory. I wish to use VMD to make a
> > movie of its time evolution. I also wish to use the Trajectory
> > smoothing window size option in VMD to make the movie less frenetic
> appearing.
> >
> >
> >
> > I have tried setting the trajectory smoothing window size to 10, since
> > it gives me a nice, smooth trajectory visualization. However, when I
> > use the Movie Maker extension/ plugin to make a movie of this smoother
> > playback of the trajectory, it seems to ignore the smoothing.
>
> there is nothing in the movie maker script (it is surprisingly simple at
its core)
> that would interfere with the smoothing settings that you have done for
> your representation.
>
> also from how trajectory smoothing is implemented, it is extremely
difficult
> to imagine how that should not work.
> there has to be some inconsistency on your side that results in VMD not
> doing what you expect because you actually didn't do it, but thought it
was
> done or something similar.
>
> axel.
>
>
>
>
>
> >
> >
> >
> > Is VMD capable of producing a movie from this smoothed representation
> > of the trajectory? If yes, how do I accomplish this? If not, is
> > there an alternative method for generating a smoothed movie of the
> > gromacs trajectory?
> >
> >
> >
> > Thanks for any help.
> >
> >
> >
> > Jim
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.