 GaMD production, NVT, 300K 20 ns each
 &cntrl
  imin=0,           ! Molecular dynamics
  irest=1,          ! Restart calculation
  ntx=5,            ! Positions and velocities read NetCDF (or formatted)
  ioutfm=1,         ! Write binary NetCDF trajectory
  nstlim=5000000,   ! Number of MD steps - 20 ns total at 4 fs timestep
  dt=0.004,         ! Timestep (ps)
  ntt=3,            ! Langevin dynamics
  gamma_ln=5.0,     ! Collision frequency for Langevin dynamics
  ig=-1,            ! Random seed for Langevin dynamics
  tempi=300.0,      ! Simulation temperature (K)
  temp0=300.0,      ! Simulation temperature (K)
  ntb=1,            ! Constant volume periodic boundary conditions
  ntc=2,            ! SHAKE on for bonds with hydrogen
  ntf=2,            ! No force evaluation for bonds with hydrogen
  cut=10.0,         ! Nonbonded cutoff (Angstroms)
  tol=0.000001,     ! SHAKE tolerance
  ntpr=25000,       ! Print to mdout every ntpr steps
  ntwr=25000,       ! Write a restart file every ntwr steps
  ntxo=2,           ! Write binary restart file
  ntwx=25000,       ! Write to trajectory file every ntwx steps
  ntwprt=<n_atoms>, ! Output only the first numATOMS atoms to trajectory files (excludes solvent)
  iwrap=1,	    ! Wrap solvent water molecules
  ntr=0,	    ! Atom restraint flag off
  igamd=3,	    ! Gaussian accelerated MD with boosts applied to total and dihedral potentials
  iE = 1,	    ! Set threshold energy E to lower bound E = Vmax
  irest_gamd = 1,   ! Restart flag for GaMD simulation; this is a continuation
  ntcmdprep= 0,     ! Number of preparation steps for cMD; potential energies not collected
  ntcmd = 0,        ! Number of cMD steps; must be multiple of ntave
  ntebprep= 0,      ! Number of preparation steps for GaMD; potential statistics not updated
  nteb = 0,         ! Number of GaMD biased steps; set to nstlim here; must be multiple of ntave
  ntave = 250000,   ! Number of steps used to calculate Ave & SD of potential energies; appx. 4x number of atoms in system
  sigma0P = 6.0, 
  sigma0D = 6.0, 
 &end
