Metadynamics simulations of twist in ApT and GpC sequence with and without H-NS bound

Metadynamics production runs were conducted using GROMACS 2023.2 patched with PLUMED-2.9.0, incorporating the RBB-NA code available on GitHub. The RBB-NA algorithm enables control of rigid base parameters in all-atom nucleic acid simulations, allowing manipulation of DNA’s six rotational parameters (tilt, roll, twist, buckle, propeller, and opening) and six translational parameters (shift, slide, rise, shear, stretch, and stagger). The twist of the central step (6th base pair) was used as the collective variable (CV). Gaussian potentials with a width of 0.04 radians and a height of 0.1 kJ/mol were deposited every 4 ps, with the bias applied only within the 10°–60° interval to prevent complete DNA denaturation at extreme twist values.