~Details~
I have a file.pdb that contains 10 frames but each frame don’t have same data size(ex. frame1 has 10 atoms, frame2 has 20 atoms….). I need a way to make animation of this file, but VMD recognize this file has just one frame. I know difference of data size in each frame is cause this problem,but I couldn't change data size. Could you solve this problem?
~I expected~ VMD recognize file.pdb contains 10 frames even thought data size is different in each frame, and I can make the animation. But VMD recognize it contains just one frame. So I couldn't.
VMD may be struggling to recognise the pdb file as a multiframe pdb due to the dataframe issue you described. One possible solution may be to split the coordinates and trajectories into two files (for example, a .gro and a .xtc as you may see in gromacs files)
This might create the added complication of needing your coordinate file to incorporate all atoms, then you may have to experiment with not assigning xyz coordinates to atoms until given timesteps, or assigning them to different residues and making them invisible at given timesteps.