; Run control integrator = sd ; Langevin dynamics tinit = 0 dt = 0.002 nsteps = 500000 ; 1 ns nstcomm = 100 ; Output control nstlog = 500 nstenergy = 100 nstxout-compressed = 0 ; Neighborsearching and short-range nonbonded interactions cutoff-scheme = verlet nstlist = 5 ns_type = grid pbc = xyz rlist = 1.2 ; Electrostatics coulombtype = PME rcoulomb = 1.2 ; van der Waals vdwtype = cutoff vdw-modifier = potential-switch rvdw-switch = 1.0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t = 1.0 ref_t = 300 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p = 1.0 compressibility = 4.5e-05 ref_p = 1.0 ; Do not generate velocities gen_vel = no ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NVT continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12