Molecular Dynamic Animation :

To specify that we want a molecular dynamic animation, three parameters have to be defined.
a) Upload a trajectory file, you can specify three types of trajectories : .xtc, .dcd and .crd
b) Choose "DM" in the scenarii menu field. Keep camera to simple
c) Define the desired number of frames from the trajectory to be animated, and the step between each frame. For our example, we used the PDB file 1BTA with no hydrogens (1BTA_noh2o.pdb), and a trajectory file of type .xtc computed with Gromacs. The trajectory was post-processed to remove the water and skip half of the frames (1BTA_md_noh2o.xtc). The title of this animation is "1BTA DYNAMIC test with 15frames" and is colored in "blue" (advanced parameters->Title options->Color). As the title says, we will only produce a test animation with 15 frames with the default representation.

The background is set to "t_cloudy_sky" (or whatever you want).
To set the animation properly, we chose the output image format as "gif" and the animation type as "DM". You can adjust the orientation of the structure by adding small rotations (in degrees) in the central cell with the chains field specified to "All". For the test we let all the rotation angle values to "0.0".
Now click on the Process button to launch the rendering. Be patient during the upload of the trajectory and during the process...
Here is what you get: