title = first full (wet) simulated annealing run ; for running on Linux cpp = /usr/bin/cpp define = -DFLEXIBLE -DFLEX_SPC -DDISTRES_DHFR -DDISTRES_NADPH constraints = all-bonds constraint_algorithm = lincs lincs_order = 4 lincs_iter = 4 integrator = md ; 30.3 ps nsteps = 22000 dt = 0.003 nstlist = 3 comm_mode = angular nstcomm = 1 comm_grps = !SOL ns_type = grid morse = no pbc = xyz ; box: 8.0 8.0 9.6 coulombtype = PME fourierspacing = 0.1 pme_order = 10 vdwtype = switch DispCorr = EnerPres ; rvdw (maybe rvdw_switch) needs to be at least 1.4 when using GROMOS96 FFs rvdw_switch = 1.4 rlist = 3.95 rcoulomb = 3.95 rvdw = 3.65 ; temperature coupling tcoupl = berendsen tc_grps = water_no_freeze_atoms !SOL water_full_freeze_atoms water_partial_freeze_atoms tau_t = 0.03 0.3 0 0 ; the below line should not actually be needed, but gromacs errors out otherwise... ref_t = 298 298 0 0 ; velocity generation gen_vel = yes gen_temp = 298 gen_seed = 173531 ; simulated annealing annealing = single single no no annealing_npoints = 6 6 0 0 annealing_time = 0 3 18 33 48 63 0 3 18 33 48 63 annealing_temp = 298 373 280 187 94 0 298 373 280 187 94 0 ; create.freezegrps.2.pl run with $freeze_more == 1 freezegrps = water_freeze_atoms freezedim = Y Y Y ; spread things out a bit nstxout = 1000 nstvout = 1000 nstlog = 1000 nstenergy = 1000 ; distance restraints disre = simple disre_weighting = equal disre_mixed = yes disre_tau = 1 nstdisreout = 1000 ; energy groups energygrp_excl = water_full_freeze_atoms water_full_freeze_atoms energygrps = water_full_freeze_atoms water_partial_freeze_atoms water_no_freeze_atoms !SOL