# Core options
T = 296.15K
steps = 10000
conf_file = start.conf
topology = generated.top # starting topology file
trajectory_file = output.dat # where the trajectory WILL be outputted
time_scale = linear
print_conf_interval = 100
print_energy_every = 100
interaction_type = DNA
seed = 0
lastconf_file = last_conf.dat
list_type = no
restart_step_counter = true
energy_file = energy.dat

# Molecular dynamics options
sim_type = MD
backend = CPU
thermostat = langevin
newtonian_steps = 1
diff_coeff = 2.5
dt = 0.003
refresh_vel = true

# Common options for DNA simulations
use_average_seq = true # FIXME: bug. if set to true, asks for a seq_dep_file

# confGenerator options
generate_consider_bonded_interactions = true

# oxDNA observables
data_output_1 = {
  name = split_energy.dat
  print_every = 100
  col_1 = {
          type = step
          units = MD
  }
  col_2 = {
          type = potential_energy
          # type = pair_energy
          split = true
  }
}
data_output_2 = {
  name = potential.dat
  print_every = 100
  col_1 = {
          type = step
          units = MD
  }
  col_2 = {
          type = potential_energy
          split = false
  }
}
data_output_3 = {
  name = pair.dat
  print_every = 100
  col_1 = {
          type = step
          units = MD
  }
  col_2 = {
          type = pair_energy
          split = false
  }
}
