VMD-L Mailing List

From: Nuno Ricardo Loureiro Ferreira (nunolf_at_ci.uc.pt)
Date: Wed Dec 13 2006 - 03:31:54 CST

Hi Russel

First of all, what you did saw was vmd loading the trajectory.
Second, in order to make a movie, use the plugin Movie Maker (Extensions.Analysis.RMSD *)
I suggest that before making the movie, you should do a protein alignement for all frames of your trajectory. This way, you are ensuring that the protein is "always" inside the display windows (basically you are removing protein diffusion). You can do this, again by using a vmd implemented plugin (Extensions.Visualization.Movie Maker).

If you are thinking of doing a movie with the solvent, just take care (the same for protein only)! You will need RAM if you want a step by step movie case. You could play with trajectory step, using for example every 10th frame of the original traj.

Cheers
Nuno

P.S. Just read it. 250 frames should not be a problem, even if you use the complete system.
  ----- Original Message -----
  From: bertrand russell
  To: vmd-l_at_ks.uiuc.edu
  Sent: Wednesday, December 13, 2006 8:36 AM
  Subject: vmd-l: How to make movie with .crd files?

  hai all,

            I am trying to make a movie in VMD using amber .crd files. My .crd files contains information of coordinates and velocities and I used periodic boundary condition while doing molecular dynamics simulation. These are the steps I followed to make the movie,

  1. I loaded the .pdb file
  2. file>load data into molecule> I loaded the .crd file
  3. My molecule was moving randomly and very rapidly. It not seems to be a movie.

  My crd file is having 250 frames.

  could anyone help me to make a moive with detailed procedure? Thanks in advance.

  --
  Live Life; Don't pass it
  Bertrand.P.S.Russell