mdp

The system was first minimized (em.mdp) and equilibrated (nvt.mdp then npt.mdp). Then a long equilibrium run (20 ns) was performed (prod.mdp). 100 snapshots were extracted every 200 ps from the equilibrium run to initialize 100 NES transitions. To decouple the alchemical water (forward direction), Coulomb interactions were first turned off over 250 ps (transition_A2B_coul_250ps.mdp) and then van der Waals (vdW) interactions (transition_A2B_vdw_250ps.mdp). To recouple the alchemical water (backward direction) the order was the opposite: first turning on vdw interactions (transition_B2A_vdw_250ps.mdp) and then Coulomb interactions (transition_B2A_coul_250ps.mdp).