; ; MDP file for GMX 4.6.7 ; integrator = md ; dt = 0.001 ; ps nsteps = 500000 ; total time: 500 ps tinit = 0 ; initial time, ps nstcomm = 1 ; freq. for cm-motion removal ld_seed = -1 ; ; Bond constraints continuation = yes ; continue from npt equilibration constraints = all-bonds ; constrain hydrogen bond lengths constraint_algorithm = lincs ; default lincs_order = 4 ; default ; X/V/F/E outputs nstxout = 500000 ; pos out --- 1000 ps nstvout = 500000 ; vel out --- 1000 ps nstfout = 0 ; force out --- no nstlog = 10000 ; energies to log (20 ps) nstenergy = 10000 ; energies to energy file nstxtcout = 10000 ; xtc, 10 ps xtc_precision = 1000 ; Neighbour list ns_type = grid ; neighlist type nstlist = 5 ; Freq. to update neighbour list rlist = 0.8 ; nm (cutoff for short-range NL) ; Coulomb interactions coulombtype = Reaction-field ; Particle Mesh Ewald epsilon_rf = 5.6 ; ClBz rcoulomb = 1.4 ; nm (direct space sum cut-off) optimize_fft = yes ; optimal FFT plan for the grid ; van der Waals interactions vdwtype = Cut-off ; Van der Waals interactions rvdw = 1.4 ; nm (LJ cut-off) DispCorr = EnerPres ; use dispersion correction ; Temperature coupling Tcoupl = Berendsen ; This is ignored with sd integrator tc-grps = System ; tau_t = 0.1 ; ps, recommended value for sd ref_t = 298.15 ; K ; Energy monitoring energygrps = System ; Pressure coupling Pcoupl = Berendsen ; Pcoupltype = isotropic ; tau_p = 0.5 ; ps compressibility = 7.45e-5 ; 1/bar (ClBz @ 1 atm, 300 K) CRC Handbook ref_p = 1.0 ; bar refcoord_scaling = all ; ; Generate velocites in the beginning gen_vel = no ; continue from npt equilibration gen_temp = 298.0 ; gen_seed = 438721 ;