# This is a sample input ark file for simulations on Anton @PSC
#
# 09/13/2010: Initial creation - Markus Dittrich
# 02/14/2011: Updates for anton_software version 2.4.* and 
#             economy_flow - Markus Dittrich
#

# equilibrated system file in maestro format
# plaese us absolute paths for the input file
# location
boot.file=sys0.cms

anton {
  chem {

    # the below two options are required for NVE
    thermostat_interval=0
    barostat_interval=0

    # this is required for NPT simulations and describes
    # how much the simulation cell is allowed to fluctuate
    # in size. Please note the increasing this values will
    # increase the memory footprint and potentially slow
    # down simulations
    max_strain = 0.08


    # increasing Escale and Fscale from the guessed values
    # may be neccessary to handle run-time errors of the form
    # 
    # LOCAL FATAL ERROR: CORR_ERR_LOG/PPIP_OVF=0x1
    #
    # The following values, e.g., are required for the bpti.cms
    # example on the Anton wiki. The initially guessed values
    # are 1000/3000 for Escale/Fscale.
    #
    # Escale = "2000.0000"
    # Fscale = "4000.0000"
  }
   
  tune {

     # use this for the 64 node Anton. On the production
     # anton use [8 8 8] instead
     machine_size = [8 8 8]

 
     regenerateBondProgram = "true"
     go_verbosity = 0
     check_overflow = "true"

     # last time step in picoseconds, use Inf to 
     # simulate forever
     last_time = Inf 

     # specify trajectory output
     # outdir   = name of output directory
     # interval = output interval in ps
     # first    = first frame to be dumped in ps
     trajectory = {
       outdir=run.atr  # Please do not change - it has to be run.atr
       interval = 50 
       first = 0 
       format=dtr   
       periodicfix = true
     }
  } 
}

# describe the integrator to be used for the simulations.
# Please note that a plain NVE simulation can be significantly
# faster than a simulation in a NVT or NPT ensemble.
# Supported values are:
#
# - V_NVE  : NVE ensemble
# - Ber_NVT: NVT ensemble with a Berendsen thermostat
# - Ber_NPT: NPT ensemble with a Berendesn thermostat/barostat
# - NH_NVT : NVT ensemble using Nose-Hoover thermostat
#
integrator {
  # specify which integrator to use
  type = Ber_NPT

  # general options
  dt=0.0020
  remove_com_motion         = true
  respa={ bonded_interval        =1
          nonbonded_near_interval=1 
          nonbonded_far_interval =3 
  }

  # V_NVE has not options 
  V_NVE = {}

  # parameters for Ber_NPT
  Ber_NPT = { 
      thermostat_molecular_ke=true
      barostat = {
         kappa = 4.5e-05
         max_expansion_per_step = 1.05
         min_contraction_per_step = 0.97
         tau = 10.0
      }
      max_velocity_scaling = 1.2
      min_velocity_scaling = 0.85
      tau = [10.0 ]
   }

   # parameters for Ber_NVT
   Ber_NVT = {
      thermostat_molecular_ke="true"
      max_velocity_scaling = 1.2
      min_velocity_scaling = 0.85
      tau = [1.0 ]
   }

   # parameters for NH_NVT
   NH_NVT = {
	     thermostat_molecular_ke="true"
             thermostat=[{mts="2"
                          tau=["1."
                               "1."
                               "1."]}]}
             

   # specify pressure for NPT ensembles, can be non-isotropic
   # (see Desmond manual)
   pressure = {
     isotropy                = semi_isotropic  # or semi_isotropic
     max_margin_contraction  = 0.9        # Maximum contraction ratio
     p_ref                   = 1          # in BAR
   }

   # system temperature
   temperature=[ {T_ref=300} ]

}