The energies of the resulting RNA polymerase and DNA gyrase unit cells of 396,776 atoms and 205,883 atoms, respectively, were then minimized by GROMACS 2016.3 and 2018.2 respectively, using a steepest descent algorithm for 1,000 steps before being gradually warmed from 100 K to 310 K over 500 ps. For comparison, the DHFR unit cell only contained 27,115 atoms . The resulting structure and velocities were used to seed three RNAP and five DNAG equilibration simulations, each 50 ns long. The temperature was maintained at 310K using a Langevin thermostat with a time constant of 2 ps. An isotropic Parrinello-Rahman barostat with a 1 ps time constant and a compressibility of 4.46 x 10 -5 bar -1 was applied to keep the pressure at 1 bar. Electrostatic forces were calculated using the particle mesh Ewald algorithm with a real space cutoff of 1.2 nm whilst van der Waals forces were only calculated between atoms less than 1.2 nm apart with a switching function applied from 0.9 nm. The lengths of all bonds involving a hydrogen were constrained using LINCS , permitting a timestep of 2 fs. For DNA gyrase, to prevent the moxifloxacin coordinated Mg 2+ from dissociating from moxifloxacin, we used a harmonic distance restraint of sufficient strength (100,000 kJ mol -1 nm -2 ) to maintain the distance observed in the crystal structure (0.209 nm) throughout all simulations, lower values were not sufficient. A series of assumed independent structures were obtained by saving the coordinates of the system every 10 ns from each of three RNAP equilibration simulations and each of five DNAG equilibration simulations.