From: Arham Amouie (erham65t_at_REMOVE_yahoo.com)
Date: Sun Jan 10 2021 - 04:17:35 CST

Hello

I use VMD 1.9.3 on Kubuntu 20.04 on a rather old laptop. I'm trying to make a simple animation from hundreds of xyz files produced with a simulation. Here is the script for rendering the frames:

display resize 389 343
display nearclip set 0.001
set indir "in/"
set outdir "images/"
for {set filenum 0} {$filenum <= 692} {incr filenum 1} {
    mol new [format "%s%05d.xyz" $indir $filenum] type {xyz} first 0 last -1 step 1 waitfor -1

    molinfo top set {center_matrix rotate_matrix scale_matrix global_matrix} {{{1 0 0 -885.859} {0 1 0 -750.065} {0 0 1 -750.047} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} {{0.00180681 0 0 0} {0 0.00180681 0 0} {0 0 0.00180681 0} {0 0 0 1}} {{1 0 0 0.78} {0 1 0 0.05} {0 0 1 0} {0 0 0 1}}}
    rotate x by $filenum
   
    mol modstyle 0 top Points 1.000000
    render snapshot [format "%s%05d.tga" $outdir $filenum]
    mol delete top
}

Each xyz file contains ~1.5 million atoms and I'm sure that the xyz files are not corrupted.

Now, the problem is that some of the rendered images are irrelevent/wrong. For example, some of the saved frames show a black screen with VMD logo on it. I also used 'display update' and 'sleep 2' before the render command, but they didn't help.

Kind regards,
Arham Amouei