title = second hetatm-only minimization (with protein H now) ; for running on Linux cpp = /usr/bin/cpp define = -DFLEXIBLE -DFLEX_SPC -DDISTRES_NADPH constraints = none integrator = cg nstlist = 5 comm_mode = angular nstcomm = 1 ns_type = grid morse = no pbc = xyz coulombtype = PME fourierspacing = 0.1 pme_order = 6 vdwtype = switch DispCorr = EnerPres ; rvdw (maybe rvdw_switch) needs to be at least 1.4 when using GROMOS96 FFs rvdw_switch = 1.4 ; box: 8.0 8.0 9.6 rlist = 3.95 rcoulomb = 3.95 rvdw = 3.65 ; energy minimization - 56 is atoms in NADPH in GROMOS96 FF emtol = 56.0 emstep = 0.01 nstcgsteep = 333 ; XXX am not sure about below... freezegrps = Protein-H freezedim = Y Y Y ; spread things out a bit nstxout = 500 nstvout = 500 nstlog = 500 nstenergy = 500 ; distance restraints disre = simple ; switch to equal for SA disre_weighting = conservative ; use for SA ; disre_mixed = yes ; try 10 for SA? disre_tau = 0 nstdisreout = 500