NVT production run
&cntrl
  imin     = 0,        ! not a minimization
  irest    = 0,        ! do not restart; run new simulation with old crds
  ntx      = 1,        ! read only crds, no velocities
  ntb      = 1,        ! NVE=0, NVT=1, NPT=2
  cut      = 12.0,     ! non-bonded cutoff (LJ)
  ntc      = 1,        ! constrain bonds involving H (SHAKE)
  ntf      = 1,        ! omit bonds involving H from forces (with NTC=2)
  temp0    = 298.00,   ! final thermostat temp in Kelvin
  tempi    = 298.00,   ! initial thermostat temp in Kelvin
  ntt      = 3,        ! Bussi (11); Langevin (3)
  ig       = -1,       ! seed for the (pseudo) random number generator
  gamma_ln = 2.0,      ! Langevin thermostat collision frequency
  ifqnt    = 1,        ! QMMM simulation
  infe     = 1,        ! Nonequilibrium free energy
  nstlim   = 500000,   ! Number of steps (nstlim * dt = run length in ps)
  dt       = 0.001,    ! timestep
  !ntwv     = -1,      ! Combines crds/vels in NetCDF file
  ntpr     = 1,        ! print to mdout file every ntpr steps
  ntwx     = 1,        ! write mdcrd file every ntwx steps
  ntwr     = 1000,     ! write restart file every ntwr steps
/
&qmmm
  qmmask     = ':1-2',
  qm_ewald   = 0,
  qmcharge   = 0,
  qm_theory  = 'AM1',
  qmcut      = 8.0,
/
&smd
  output_file   = 'smd.txt',
  output_freq   = 1,
  cv_file       = 'cv_LCOD.in',
/