GROMACS to Blender script, and maybe more in the future
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  • Copy to ~/.blender/scripts

  • Create a directory for per-frame pdb files and name it the same as the structure (e.g. "c60")

  • Each per-frame pdb file should be named with the frame number and ".pdb" extension. e.g. "1.pdb" through "999.pdb" and placed in the "c60" directory

  • Run the script, choose your structure file (e.g. "c60.pdb")

  • Advancing the frames will animate the structure

  • To create the pdb frames from GROMACS, use the trjconv program:

       trjconv -s <structure> -f traj.trr -o .pdb -sep