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 starting 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