title = initial water-only minimization ; for running on Linux cpp = /usr/bin/cpp define = -DFLEXIBLE -DFLEX_SPC -DDISTRES_NADPH constraints = none ; this is for only the initial one - for further, use cg integrator = steep nstlist = 5 comm_mode = angular nstcomm = 1 ns_type = grid morse = no pbc = xyz coulombtype = PME fourierspacing = 0.1 ; enable below when doing further steps ; 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 emtol = 500.0 emstep = 0.01 freezegrps = Protein freezedim = Y Y Y energygrp_excl = Protein Protein energygrps = Protein Other ; 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