; VARIOUS PREPROCESSING OPTIONS title = normIons ;cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS integrator = sd ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 250000 ; 0.5ns authorized production; original 5ns ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 100 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Checkpointing helps you continue after crashes ; Removed legacy option: nstcheckpoint ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file nstxout-compressed = 1000 compressed-x-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. compressed-x-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ;match Karisa ; ns algorithm (simple or grid) ; Removed legacy option: ns_type ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.2 ;domain-decomposition = no ; match Karisa ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb-switch = 0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field ;epsilon-r = 1 ; match Karisa ; Method for doing Van der Waals vdw-type = Cut-off vdw-modifier = Potential-switch cutoff-scheme = Verlet coulomb-modifier = None sc-function = beutler ; cut-off lengths rvdw-switch = 0.9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure ;DispCorr = EnerPres ; Match Karisa DispCorr = AllEnerPres ; Extension of the potential lookup tables beyond the cut-off ;table-extension = 1 ; match Karisa ; Spacing for the PME/PPPM FFT grid ;fourierspacing = 0.12 fourierspacing = 0.10 ; Match Karisa ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters ;pme_order = 4 ; Match Karisa pme_order = 6 ;ewald_rtol = 1e-05 ewald_rtol = 1e-06 ; Match Karisa ewald_geometry = 3d epsilon_surface = 0 ;optimize_fft = no ; Removed legacy option: optimize_fft ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = no ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 2.0 ref_t = 298.15 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 10 compressibility = 4.5e-5 ref_p = 1.01325 ; Random seed for Andersen thermostat andersen_seed = 815131 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ;gen_temp = 298.15 ;gen_seed = 1993 ld_seed = -1 ; OPTIONS FOR BONDS constraints = hbonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration continuation = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix ;lincs-order = 4 lincs-order = 12 ; Match Karisa ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. ;lincs-iter = 2 ; Removed to Match Karisa ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = ; Free energy control stuff free-energy = yes init_lambda_state = 10 fep_lambdas = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 vdw_lambdas = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 couple-moltype = MOL couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no sc-alpha = 0.5 sc-sigma = 0.3 sc-power = 1 sc-coul = no nstdhdl = 100 calc-lambda-neighbors = -1