; VARIOUS PREPROCESSING OPTIONS = title = Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS = integrator = md ; ; for polarizable water minimization do not forget to replace the ; constraints by stiff bonds (force constant of 50000) ; ; start time and timestep in ps = tinit = 0.0 dt = 0.020 ; ; Polarizable water is stable with 30 fs timestep ; nsteps = 1000000 ; number of steps for center of mass motion removal = ;nstcomm = 1 ;comm-grps = ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 100 ; Output frequency and precision for xtc file = nstxtcout = 5000 xtc_precision = 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = PW ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = ;coulombtype = PME coulombtype = shift rcoulomb = 1.2 ; ; Polarizable water may be used with standard Martini shift, but also with PME ; rcoulomb_switch = 0.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 2.5 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 10 fourier_ny = 10 fourier_nz = 10 ; EWALD/PME/PPPM parameters = pme_order = 4 ewald_rtol = 1e-05 epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; v-rescale ; Groups to couple separately = tc-grps = system ; Time constant (ps) and reference temperature (K) = tau_t = 0.3 ref_t = 300 ; Pressure coupling = Pcoupl = Berendsen ; Parrinello-Rahman Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 3.0 compressibility = 3e-5 ref_p = 1.0 ; SIMULATED ANNEALING CONTROL = annealing = no ; Time at which temperature should be zero (ps) = zero_temp_time = 0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 325 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Relative tolerance of shake = shake_tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 90 ; ; for polarizable water sometimes Lincs warnings appear for no apparent reason ; with a warnangle of 90 this is largely avoided