VMD-L Mailing List

From: Mauricio Carrillo Tripp (trippm_at_gmail.com)
Date: Thu Apr 07 2005 - 08:39:14 CDT

How many steps/frames do you have on your trajectory?
Remember that you need 30 frames/snapshots per second
on the final mpeg movie. If you want it to go slower, you need
to insert more frames inbetween to achieve the speed you want
(This means you need to save the steps in your trajectory more
frequently or in a post simulation fashion, maybe interpolating
each step to get more frames inbetween). Here is something I
wrote yesterday, maybe it will help you:

Actually, the movie maker is an editable script that vmd runs. You
could modify that
script to do what you need. Or work your way around it, but you might need
a simple script at some point (just to make things easier and faster). What
you need to know is that you need 30 frames (or snapshots) per second in
the final movie (mpeg). What the movie maker script does, is to generate a
lot of snapshots (each one slightly different from the one before, as to
create
the effect of movement in the final movie file. Of course these 'frames'
don't
have to be different from each other, they can be the same one duplicated
many times, and the effect this would do in the final movie file is that
your
molecule would appear to be 'frozen'). The last thing the movie maker script
does is to merge all the snapshots into one file (with the correct format,
mpeg
for example) using an external tool (ppmtompeg in linux). If you do this,
tell
the movie maker script not to delete the files it creates on the menu
options
so you can use them later. Make a snapshot of the first frame and duplicate
it
as many times as you need (30 times per each second you want on the movie).
Name them sequentially, lets say you want 2 seconds, then you will need
60 files, named something-0001.ppm to something-0060.ppm (you also need
to rename the frames vmd creates so they start at something-0061.ppm to
whatever number of frames vmd made, if it initially made 180 frames, then
the last frame would be something-0240.ppm). Now edit the file vmd created
with extension .par (something.par), changing the input section to include
all your frames:
INPUT
something-*.ppm [0001-0240]
END_INPUT
Now run 'ppmtompeg something.par', that should give you a file
something.mpg where the first 2 seconds are a 'frozen' molecule and after
that
it will start to move!

On Apr 7, 2005 4:08 AM, Chaitanya Krishna A <icymist82_at_yahoo.com> wrote:
>
> Hi all,
>
> I have a small problem. I am not much into molecular
> dynamics yet. But I have just started writing my own
> coded to some simple simulations of Ar and a binary
> mixture.
>
> I am also quite new to using VMD.
>
> I am using VMD to play the trajectory of my 864 atom
> Ar system.
>
> The way I am doing it is as follows:
> After the simulation I have all the coordinates of all
> the 864 atoms for all the time steps sequentially in
> the xyz format. I am using babel to convert into the
> pdb format and then invoking VMD with the command
> $ vmd <pdb file name>
> Now it loads all the frames and then I use the movie
> maker to make the movie of the trajectory of the 864
> atoms. VMD makes an mpg movie.
>
> The problem is that when I play the mpg movie that VMD
> makes, it runs very fast before one can actually
> realise what is happening. I have been using xine to
> play the movie. It would be nice if someone can
> suggest how I can slow down the speed of the mpg
> movie.
>
> I would also like to know if there's any better way of
> making the movie different from the one that I
> described above.
>
> Thanks for any help and your time.
> Chaitanya.
> Indian Inst. of Science, India.
>
>
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> 

-- 
Mauricio Carrillo Tripp, PhD
Department of Chemistry
Wabash College
trippm_at_wabash.edu
http://chem.acad.wabash.edu/~trippm <http://chem.acad.wabash.edu/%7Etrippm>