General simulation parameters

All simulations were performed at constant temperature (either 300 or 320 K) and pressure (1 atm) using a Langevin thermostat and barostat. NAMD’s default switching function at 1.0 nm was used to smoothly truncate nonbonded interactions at 1.2 nm. Electrostatic forces were calculated using particle mesh Ewald on a grid with a 1.0 Å spacing. The 1–4 scaling was set to 0.8333 for simulations with ff12SB to match AMBER’s nonbonded exclusion convention. The velocity Verlet algorithm with a 2 fs time step was used to integrate the equations of motion. Coordinates and energies were saved every 1 ps.