# Program parameters
sim_type = MD
backend = CPU
CUDA_list = verlet
CUDA_sort_every = 0
use_edge = true
seed = 83
cells_auto_optimisation = false
max_density_multiplier = 10
# verlet_skin = 0.5
verlet_skin = 0.1
interaction_type = RNA2
dh_half_charged_ends = False
list_type = no
# external_model = external_model.txt

# Simulation parameters
steps = 10000
newtonian_steps = 103
diff_coeff = 2.5
thermostat = john
dt = 0.003
ensemble = nvt
T = 296.15K
salt_concentration = 1.0

use_average_seq = 0
seq_dep_file = rna_sequence_dependent_parameters.txt

# Input/output
topology = sys.top
conf_file = init.conf
lastconf_file = last_conf.dat
refresh_vel = 1
log_file = sim.log
no_stdout_energy = 0
restart_step_counter = 0
energy_file = energy.dat
print_conf_interval = 500
print_conf_ppc = 51
print_energy_every = 500
trajectory_file = output.dat
time_scale = linear




# oxDNA observables
data_output_1 = {
  name = split_energy.dat
  print_every = 500
  col_1 = {
          type = step
          units = MD
  }
  col_2 = {
          type = potential_energy
          # type = pair_energy
          split = true
  }
}
data_output_2 = {
  name = potential.dat
  print_every = 500
  col_1 = {
          type = step
          units = MD
  }
  col_2 = {
          type = potential_energy
          split = false
  }
}
data_output_3 = {
  name = pair.dat
  print_every = 500
  col_1 = {
          type = step
          units = MD
  }
  col_2 = {
          type = pair_energy
          split = false
  }
}
