Cluster:Pymol

Once you have run: grompp -f file.mdp -p topol.top -o file.tpr

Which takes in a run configuration mdp file, and a system topology file, topol.top and outputs a tpr file.

And after running the simulation: mdrun -deffnm run

Convert the gromacs trajectory file to a pdb file: trjconv -s run.topr -f lowpass.xtc -o file.pdb

In order to just view the molecule being simulated select protein for the output group.

Run pymol on the created pdb file: pymol file.pdb

Control pymol with the VCR buttons