Hi, [1] CHARMM36 is to be used with the CHARMM-modified TIP3P water model (TIP3P with LJ parameters on the water molecule hydrogen atoms). [2] By default it's rigid, but check "define =" under your mdout.mdp file. If there's no -DFLEXIBLE, then it's rigid. [3] No idea of what that is, sorry. Cheers, J