A NPT simulation for common production-level simulations
 &cntrl
    imin=0,        ! No minimization
    irest=1,       ! This IS a restart of an old MD simulation
    ntx=5,         ! So our inpcrd file has velocities

    ! Temperature control
    ntt=3,         ! Langevin dynamics
    gamma_ln=1.0,  ! Friction coefficient (ps^-1)
    temp0=310,     ! Target temperature
    ig=-1,         ! The random seed will be based on the current date and time, and hence will be different for every run

    ! Potential energy control
    cut=8.0,       ! nonbonded cutoff, in Angstroms
    ntb=2,         ! periodic boundary conditions for calculation of non-bonded interactions

    ! MD settings
    nstlim=500000, ! 500K steps, 1 ns total
    dt=0.002,      ! time step (ps)

    ! SHAKE
    ntc=2,         ! Constrain bonds containing hydrogen
    ntf=2,         ! Do not calculate forces of bonds containing hydrogen
    tol=0.0000001, ! SHAKE tolerance

    ! Control how often information is printed
    ntpr=2500,     ! Print energies every 2500 steps
    ntwx=2500,     ! Print coordinates every 2500 steps to the trajectory
    ntwr=2500,     ! Print a restart file every 2500 steps (can be less frequent)
    ntwe=2500,     ! Pring energies and temperatures every 2500 to file "mden"
!   ntwv=-1,       ! Uncomment to also print velocities to trajectory
!   ntwf=-1,       ! Uncomment to also print forces to trajectory
    ntxo=1,        ! Write Formatted (ASCII)
    ioutfm=0,      ! Formatted ASCII trajectory

    ! Wrap coordinates when printing them to the same unit cell
    iwrap=1,

    ! Constant pressure control. Note that ntp=3 requires barostat=1
    barostat=1,    ! Berendsen... change to 2 for MC barostat
    ntp=2,         ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
    pres0=1.0,     ! Target external pressure, in bar
    taup=0.5,      ! Berendsen coupling constant (ps)

    ! Constant surface tension (needed for semi-isotropic scaling). Uncomment
    ! for this feature. csurften must be nonzero if ntp=3 above
!   csurften=3,    ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
!   gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso scaling
!   ninterface=2,  ! Number of interfaces (2 for bilayer)

    ! Set water atom/residue names for SETTLE recognition
    watnam='WAT',  ! Water residues are named WAT
    owtnm='O',     ! Water oxygens are named O
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 &ewald
    skinnb=5,      ! Increase skinnb to avoid skinnb errors
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