From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Wed Mar 25 2009 - 20:37:16 CDT

Hi Lan -

I've never worked with the xyz format before but I believe VMD can
read it using the molfile plugin (it should be able to load the
coordinates via the GUI - i.e. "load data into molecule" or "new
molecule"). What you might be able to do is write a tcl script to
basically call molfile to load all the frames of your trajectory into
a single "molecule" in VMD (for lack of a better description, I am
trying to describe loading them in as sequential frames rather than
individual structures). Then you should be able to play the
trajectory and make a movie from it.

You need a psf file if you are loading compressed dcd files. If you
already have all the frames of your trajectory as xyz, it should be
loadable without the psf file, but the way VMD draws the connectivity
cannot be guaranteed to be correct.

-Eric

On Mar 25, 2009, at 6:39 PM, Lan He wrote:

> Hi Eric:
>
> Thank you again. Actually, I can use VMD to process individual xyz
> file and get still frame. Since I just use the MD codes written by
> myself to run MD, I can get the trajectory files only with xyz file
> formate. But, In VMD image and movie tutorials, .psf and .dcd files
> seem to be required. is it right? I'm totally confused. Thanks for
> your help!
>
> Best regards,
>
> Lan He
> - - - - - - - - - - - - - - - - - - - - - - - - - -
> Department of Mechanical and Aerospace Engineering
>
> Arizona State University
>
> Tempe, AZ
>
>
> ________________________________
>
> From: Eric H. Lee [mailto:ericlee_at_ks.uiuc.edu]
> Sent: Wed 3/25/2009 16:13
> To: Lan He
> Subject: Re: vmd-l: how to make a mivie by VMD
>
>
> As Anton suggested in the other email, you will likely benefit from
> first learning how to use VMD. Go through the VMD tutorial here:
>
> http://www.ks.uiuc.edu/Training/Tutorials/
>
> to learn how to load and manipulate molecules in VMD. Once you
> understand how to load structure files and trajectories, it will be
> clear how to make a movie using Moviemaker.
>
> -Eric
>
> On Mar 25, 2009, at 6:07 PM, Lan He wrote:
>
>
> Hi Eric:
>
> Thank you so much for the suggestion. But I really don't know how
> to do it -------------"load the trajectories into VMD and use the
> Moviemaker tool (Extensions > Movie Maker) to render the movie frame
> by frame".
>
> "load the trajectories into VMD and use the moviemaker tool to
> render the movie frame by frame"
> you mean, I can load all the coordinate files together into VMD
> display and save it. Then in the menu of moviemaker tool, the
> working directory is where I save the VMD display and I just click
> make movie, the mpeg file can be produced.
>
> Or, you mean that, I still load the coordinate file one by one into
> VMD display and save each into the same file. Then in the menu of
> moviemaker tool, I set the working difectory as the path for finding
> the saved frames, and click "make movie", the mpeg file can be
> produced.
>
> Could you tell me how to use moviemaker in detail? I'm very
> grateful of your help.
>
>
> Best regards,
>
> Lan He
> - - - - - - - - - - - - - - - - - - - - - - - - - -
> Department of Mechanical and Aerospace Engineering
>
> Arizona State University
>
> Tempe, AZ
>
>
> ________________________________
>
> From: Eric H. Lee [mailto:ericlee_at_ks.uiuc.edu]
> Sent: Wed 3/25/2009 15:44
> To: Lan He
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: how to make a mivie by VMD
>
>
> Probably the most simple way to make a movie since you already have
> the trajectories is to load the trajectories into VMD and use the
> Moviemaker tool (Extensions > Movie Maker) to render the movie frame
> by frame. It will produce an mpeg of your trajectory.
>
> -Eric
>
> On Mar 25, 2009, at 5:33 PM, Lan He wrote:
>
>
> Hello,
>
> I'd like to use VMD for the movie of bonding formation. I have
> coordinate files for the structure from MD simulations. Now I'm
> planing to prepare sufficient frames for the structure along MD
> evolution time at first. Since each frame for the struture at
> specific MD time has its coordinate file, I don't know how to use
> tcl script to drive render commands and produce the sequence of all
> frames.
> Next, if all frames are ready, I'd like to know if I need import
> these figure files into animation package ,such as Movie maker in
> VMD extensions. As I never make a movie for MD simulation results, I
> really have no idea about this. If you know how to use VMD for
> making movies, please kindly tell me the procedure or give me some
> advice. Thank you so much!
>
>
> Best regards,
>
> Lan He
> - - - - - - - - - - - - - - - - - - - - - - - - - -
> Department of Mechanical and Aerospace Engineering
>
> Arizona State University
>
> Tempe, AZ
>
>
>
>
> Eric H. Lee
>
> Medical Scholars Program
>
> Theoretical and Computational Biophysics Group, UIUC
>
> ericlee_at_ks.uiuc.edu
>
>
>
>
>
> Eric H. Lee
>
> Medical Scholars Program
>
> Theoretical and Computational Biophysics Group, UIUC
>
> ericlee_at_ks.uiuc.edu
>
>

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu