Production Run, 500ns with step 2fs
&cntrl
  ntt=3,           ! Temperature scaling (=3, Langevin dynamics)
  temp0 = 300,      ! target temperature
  tempi = 300,
  gamma_ln=2.0,    ! Collision frequency of the Langevin dynamics in ps-1
  ntc=2,           ! SHAKE constraints (=2, hydrogen bond lengths constrained)
  ntf=2,           ! Force evaluation (=2, hydrogen bond interactions omitted)
  ntb=2,           ! Boundaries (=2, constant pressure)
  ntp=1,             ! Constant pressure dynamics (=1, isotropic position scaling)
  barostat=1,        ! Barostat to control the pressure (=1, Berendsen)
  pres0=1.0,         ! Target pressure (1 bar)
  taup=1.0,          ! Pressure relaxation time in ps
  cut=8.0,         ! Cutoff
  dt=0.002,        ! The time step in picoseconds
  nstlim=250000000, ! Number of MD steps to be performed
  ig=-1,           ! Random seed (=-1, get a number from current date and time)
  ntwr=10000,      ! Restart file written every ntwr steps
  ntwx=10000,      ! Trajectory file written every ntwx steps
  ntpr=10000,      ! The mdout and mdinfo files written every ntpr steps
  ioutfm=1,        ! Trajectory file format (=1, Binary NetCDF)
  iwrap=1,         ! Translate water molecules into the original simulation box
  igb=0,           ! GB model (=0, explicit solvent)
  irest=1,         ! Flag to restart the simulation
  ntx=5,           ! Initial condition (=5, coord. and veloc. read from the inpcrd file)
/