Input options of the previous version

From OxDNA

Generic options

The options listed here define the generic behavior of the entire program.

[interaction_type = DNA]
(selects the model for the simulation. DNA (oxDNA model) is the default option. RNA (oxRNA model), LJ (Lennard-Jones) and patchy particles are also implemented
MD = Molecular Dynamics, MC = Monte Carlo
(only sim_type=MD is supported if you choose CUDA backend)
(mixed option is available only for CUDA backend. It is recommended choice for optimal performance on CUDA machines, double is recommended for CPU simulations)
1 if you want verbose logs, 0 otherwise.

Simulation options

The options listed here specify the behaviour of the simulation.

number of steps to be performed.
0 means that the step counter will start from the value read in the configuration file; if 1, the step counter will be reset to 0. The total duration of the simulation is unchanged.
seed for the random number generator. On Unix systems, it will use by default a number from /dev/urandom + time(NULL)
temperature of the simulation. It can be expressed in simulation units or kelvin (append a k or K after the value) or celsius (append a c or C after the value).
Value Simulation Units
0.1 0.1
300 K 0.1
300k 0.1
26.85c 0.1
26.85 C 0.1
if a particle moves more than verlet_skin then the lists will be updated. Its name is somewhat misleading: the actual verlet skin is 2*verlet_skin.
specifies whether to use the default hard-coded average parameters for base-pairing and stacking interaction strengths or not. If sequence dependence is to be used, set this to 0 and specify seq_dep_file.
specifies the file from which the sequence dependent parameters should be read. Mandatory if use_average_seq=no, ignored otherwise. A sample file is provided (sequence_dependent_parameters.txt).
specifies whether there are external forces acting on the nucleotides or not. If it is set to 1, then a file which specifies the external forces' configuration has to be provided (see external_forces_file).
specifies the file containing all the external forces' configurations. Currently there are six supported force types (see EXAMPLES/TRAPS for some examples):
  • string
  • twist
  • trap
  • repulsion_plane
  • repulsion_plane_moving
  • mutual_trap

Molecular dynamics simulations options

time step of the integration.
no means no thermostat will be used. refresh will refresh all the particle's velocities from a maxwellian every newtonian_steps steps. john is an Anderson-like thermostat (see pt). Make sure you read thermostat.
required if thermostat != no
number of steps after which a procedure of thermalization will be performed.
used if thermostat == john. It's the probability that a particle's velocity will be refreshed during a thermalization procedure.
required if pt is not specified
used internally to automatically compute the pt that would be needed if we wanted such a self diffusion coefficient. Not used if pt is set.

Monte Carlo simulations options

this number times print_energy_every gives the number of steps after which the energy will be computed from scratch and checked against the actual value computed adding energy differences.
if abs((old_energy - new_energy)/old_energy) > check_energy_threshold then the program will die and warn the user.
ensemble of the simulation. More ensembles could be added in future versions.
maximum displacement (per dimension) for translational moves in simulation units.
maximum displacement for rotational moves in simulation units.


The options listed here are used to manage the I/O (read and write configurations, energies and so on)

initial configuration file.
file containing the system's topology.
the main output of the program. All the configurations will be appended to this file as they are printed.
valid only if conf_file is a trajectory. Skip the first confs_to_skip configurations and then load in memory the (confs_to_skip+1)th.
this is the file where the last configuration is saved (when the program finishes or is killed). Set to last_conf.dat by default
if 1 the initial velocities will be refreshed from a maxwellian.
energy output file.
this will make the program print the energies every print_energy_every steps.
if 1 the energy will be printed just to the energy_file.
using linear configurations will be saved every print_conf_interval.
using log_lin configurations will be saved logarithmically for print_conf_ppc times. After that the logarithmic sequence will restart.
linear interval if time_scale == linear. First step of the logarithmic scale if time_scale == log_lin.
used if time_scale == log_lin
points per logarithmic cycle.
every print_reduced_conf_every steps the program will print out the reduced configurations (i.e. confs containing only the centers of mass of strands).
used if print_reduced_conf_every > 0
output directory for reduced_conf files.
file where generic and debug informations will be logged. If not specified then stderr will be used.
if 1 the MD step timing have be printed to a file.
used if print_timings == 1
output file where the MD step timing will be appended to.