; RUN CONTROL PARAMETERS = define = integrator = md ; start time and timestep in ps = tinit = 0.0 dt = 0.010 nsteps = 1000000 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps = System ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1000 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file = nstxtcout = 0 xtc_precision = 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = Protein ; Selection of energy groups = energygrps = System ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = simple ; Periodic boundary conditions: xyz or none = pbc = no ; nblist cut-off = rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 15 ; 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 ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = berendsen ; Groups to couple separately = tc-grps = System ; Time constant (ps) and reference temperature (K) = tau_t = 1 ref_t = 323 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 300 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; 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