Skip to content
GROMACS to Blender script, and maybe more in the future
Python
Find file
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Failed to load latest commit information.
README.md
gmx2blend.py initial
import_ipo.py
proteindb.py initial

README.md

Instructions:

  • Copy proteindb.py 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
    
Something went wrong with that request. Please try again.