prepmd 6xov 6xov_processed.cif will download the structure for PDB entry 6xov, process it and write it to 6xov_processed.cif.
runmd 6xov_processed.cif --traj_out traj.xtc --md_steps 5000 will minimise and run a simulation of 6xov_processed.cif writing a trajectory to traj_out.xtc, for 5000 steps. By default, runmd uses a minimal set of simulation parameters, which aren't likely to be accurate - check the runmd section of this documentation for more options.