Cluster:Pymol

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

Run the mdrun output through a lowpass filter to smooth out the transition of the atoms in the system between time steps:
g_filter -s run.tpr -f run.xtc -ol lowpass.xtc -nx 10 -all

Convert the gromacs trajectory file to a pdb file:
trjconv -s run.topr -f lowpass.xtc -o file.pdb
In order to view just the molecule being modeled select protein for the output group.

Run pymol on the created pdb file: pymol file.pdb
Control pymol with the VCR buttons