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This function adds energy groups to your mdp file

I essentially just copied from Alex K. Chew but I dont know C so I uhh, just put it into python please dont hate me. He has a better and more thorough way of explaining this and has an actual job so maybe look at his tutorial okay?

• first: run your simulation
• make an index file that contains your energy groups of interest and nothing else
• upload your desired md.mdp file here and enter the energy_groups that you made in the index file
• make new tpr file vide infra
• gmx grompp -f output_file.mdp -c confout.gro -p topol.top -o energy_groups.tpr -n energy_group_index.ndx
• Re-run the sim using the -rerun flag vide infra
• gmx mdrun -s penergy_groups.tpr -rerun existing_traj.trr -e energy_groups.edr
• Now use gmx energy -f energy_groups.edr to view your results
• LJ = lenny jones
• SR = short range
• Coul = you used PME so you cant decompose

Adopted from Alex K. Chew