******************************************** energy minimization ; Run parameters define = -DFLEXIBLE integrator = steep nsteps = 50000 emtol = 500 emstep = 0.01 niter = 20 nstlog = 1 nstenergy = 1 constraint_algorithm = lincs constraints = h-bonds lincs_order = 6 lincs_iter = 4 continuation = no nstlist = 1 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 vdw-type = cutoff rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = no pcoupl = no gen_vel = no ******************************************** NVT at 700 K integrator = md dt = 0.002 tinit = 0 nsteps = 500000 nstcomm = 10 pbc = xyz nstxout = 10000 nstvout = 10000 nstfout = 10000 nstlog = 10000 nstenergy = 10000 nstxtcout = 10000 xtc-precision = 10000 ; constraint_algorithm = lincs ; lincs_order = 12 ; lincs_iter = 8 ; constraints = h-bonds continuation = yes nstlist = 10 ns_type = grid rlist = 1.5 coulombtype = PME_switch rcoulomb_switch = 1.18 rcoulomb = 1.2 vdw-type = switch rvdw-switch = 1.18 rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 5 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = berendsen tc-grps = system tau_t = 0.5 ref_t = 700.0 pcoupl = no gen_vel = yes gen_temp = 700.0 ******************************************** NpT at 700 K and 1 atm integrator = md dt = 0.002 tinit = 0 nsteps = 500000 nstcomm = 10 pbc = xyz nstxout = 10000 nstvout = 10000 nstfout = 10000 nstlog = 10000 nstenergy = 10000 nstxtcout = 10000 xtc-precision = 10000 constraint_algorithm = lincs lincs_order = 6 lincs_iter = 4 constraints = h-bonds continuation = yes nstlist = 10 ns_type = grid rlist = 1.5 coulombtype = PME_switch rcoulomb_switch = 1.18 rcoulomb = 1.2 vdw-type = switch rvdw-switch = 1.18 rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 5 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = berendsen tc-grps = system tau_t = 0.5 ref_t = 700.0 pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 ref_p = 1.0 compressibility = 4.9e-5 gen_vel = no gen_temp = 700.0 ******************************************** NpT annealing from 700 K to 400 K ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 1000000 nstcomm = 10 pbc = xyz constraint_algorithm = lincs lincs_order = 6 lincs_iter = 4 constraints = h-bonds continuation = no nstxout = 10000 nstvout = 10000 nstfout = 10000 nstlog = 10000 nstenergy = 10000 nstxtcout = 10000 xtc-precision = 10000 annealing = single annealing_npoints = 7 annealing_time = 0 300 600 900 1200 1500 1800 annealing_temp = 700 650 600 550 500 450 400 nstlist = 10 ns_type = grid rlist = 1.5 coulombtype = PME_switch rcoulomb_switch = 1.18 rcoulomb = 1.2 vdw-type = switch rvdw_switch = 1.18 rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 5 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = berendsen tc-grps = system tau_t = 0.5 ref_t = 400.0 pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 ref_p = 1.0 compressibility = 4.5e-5 gen_vel = no ******************************************** NpT equilibration at 400 K and 1 atm integrator = md dt = 0.002 tinit = 0 nsteps = 5000000 nstcomm = 10 pbc = xyz nstxout = 10000 nstvout = 10000 nstfout = 10000 nstlog = 10000 nstenergy = 10000 nstxtcout = 10000 xtc-precision = 10000 constraint_algorithm = lincs lincs_order = 6 lincs_iter = 4 constraints = h-bonds continuation = yes nstlist = 10 ns_type = grid rlist = 1.5 coulombtype = PME_switch rcoulomb_switch = 1.18 rcoulomb = 1.2 vdw-type = switch rvdw-switch = 1.18 rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 5 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = nose-hoover tc-grps = system tau_t = 3.0 ref_t = 400.0 pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 3.0 ref_p = 1.0 compressibility = 4.9e-5 gen_vel = no ******************************************** NVT at 400 K integrator = md dt = 0.002 tinit = 0 nsteps = 2500000 nstcomm = 10 pbc = xyz nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout = 5000 xtc-precision = 10000 constraint_algorithm = lincs lincs_order = 6 lincs_iter = 4 constraints = h-bonds continuation = yes nstlist = 10 ns_type = grid rlist = 1.5 coulombtype = PME_switch rcoulomb_switch = 1.18 rcoulomb = 1.2 vdw-type = switch rvdw-switch = 1.18 rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = nose-hoover tc-grps = system tau_t = 3.0 ref_t = 400.0 pcoupl = no gen_vel = yes gen_temp = 400.0 ******************************************** NVE production run integrator = md dt = 0.002 tinit = 0 nsteps = 7500000 nstcomm = 10 pbc = xyz nstxout = 1000 nstvout = 0 nstfout = 0 nstlog = 10000 nstenergy = 10000 nstxtcout = 10000 xtc-precision = 10000 constraint_algorithm = lincs lincs_order = 6 lincs_iter = 4 constraints = h-bonds continuation = yes nstlist = 5 ns_type = grid rlist = 1.5 coulombtype = PME_switch rcoulomb_switch = 1.18 rcoulomb = 1.2 vdw-type = switch rvdw-switch = 1.18 rvdw = 1.2 DispCorr = EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = no pcoupl = no gen_vel = no