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Input file options

In the list below the expected type of the value is specified between < and >. A key can be specified with values 1|0, yes|no or true|false. The | symbol (pipe) is used to indicate the different values that can be used to specify a value for the key. Keys between [ and ] are optional.

Core options:

T = <float>
    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).
[fix_diffusion = <bool>]
    if true, particles that leave the simulation box are brought back in
    via periodic boundary conditions. Defaults to true.
[seed = <int>]
    seed for the random number generator. On Unix systems, defaults to
    either a number from /dev/urandom or to time(NULL)
[confs_to_skip = <int>]
    how many configurations should be skipped before using the next one as
    the initial configuration, defaults to 0
restart_step_counter = <boolean>/<bool>
    false means that the step counter will start from the value read in
    the configuration file, true means that the step counter will start
    from 0/if True oxDNA will reset the step counter to 0, otherwise it
    will start from the step counter found in the initial configuration.
    Defaults to False.
[external_forces = <bool>]
    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)
[external_forces_file = <path>]
    specifies the file containing all the external forces' configurations.
    Currently there are six supported force types: string, twist, trap,
    repulsion_plane, repulsion_plane_moving and mutual_trap (see
    EXAMPLES/TRAPS for some examples)
[back_in_box = <bool>]
    whether particles should be brought back into the box when a
    configuration is printed or not, defaults to false
[lastconf_file = <path>]
    path to the file where the last configuration will be dumped
trajectory_file = <path>
    path to the file which will contain the output trajectory of the
    simulation
[binary_initial_conf = <bool>]
    whether the initial configuration is a binary configuration or not,
    defaults to false
[lastconf_file_bin = <path>]
    path to the file where the last configuration will be printed in
    binary format, if not specified no binary configurations will be
    printed
[print_reduced_conf_every = <int>]
    every how many time steps configurations containing only the centres
    of mass of the strands should be printed. If 0, no reduced
    configurations will be printed
[reduced_conf_output_dir = <path>]
    path to the folder where reduced configurations will be printed
[no_stdout_energy = <bool>]
    if true oxDNA will not print the default simulation output, including
    the energy, to stdout. Defaults to false
[print_timings = <bool>]
    whether oxDNA should print out to a file performance timings at the
    end of the simulation or not, defaults to false
[timings_filename = <path>]
    path to the file where timings will be printed
[output_prefix = <string>]
    the name of all output files will be preceded by this prefix, defaults
    to an empty string
[checkpoint_every = <int>]
    If > 0, it enables the production of checkpoints, which have a binary
    format. Beware that trajectories that do have this option enabled will
    differ from trajectories that do not. If this key is specified, at
    least one of checkpoint_file and checkpoint_trajectory needs to be
    specified
[checkpoint_file = <string>]
    File name for the last checkpoint. If not specified, the last
    checkpoint will not be printed separately
[checkpoint_trajectory = <string>]
    File name for the checkpoint trajectory. If not specified, only the
    last checkpoint will be printed
[reload_from = <string>]
    checkpoint to reload from. This option is incompatible with the keys
    conf_file and seed, and requires restart_step_counter=0 as well as
    binary_initial_conf!=1
[print_input = <bool>]
    make oxDNA write the input key=value pairs used by the simulation in a
    file named input.pid, with pid being the oxDNA pid. Defaults to False.
conf_file = <string>
    path to the starting configuration
steps = <int>
    length of the simulation, in time steps
[equilibration_steps = <int>]
    number of equilibration steps. During equilibration, oxDNA does not
    generate any output. Defaults to 0
time_scale = linear/log_lin
    a linear time_scale will make oxDNA print linearly-spaced
    configurations. a log_lin will make it print linearly-spaced cycles of
    logarithmically-spaced configurations.
print_conf_interval = <int>
    if the time scale is linear, this is the number of time steps between
    the outputing of configurations, otherwise this is just the first
    point of the logarithmic part of the log_lin time scale
print_conf_ppc = <int>
    mandatory only if time_scale == log_line. This is the number of
    printed configurations in a single logarithmic cycle.
[print_energy_every = <int>]
    number of time steps between the outputing of the energy (and of the
    other default observables such as acceptance ratios in Monte Carlo
    simulations). Defaults to 0.
verlet_skin = <float>
    width of the skin that controls the maximum displacement after which
    Verlet lists need to be updated.
[list_type = verlet|cells|no]
    Type of neighbouring list to be used in CPU simulations. 'no' implies
    a O(N^2) computational complexity. Defaults to verlet.

MD options:

[reset_initial_com_momentum = <bool>]
    if true the momentum of the centre of mass of the initial
    configuration will be set to 0. Defaults to false to enforce the
    reproducibility of the trajectory
[reset_com_momentum = <bool>]
    if true the momentum of the centre of mass will be set to 0 each time
    fix_diffusion is performed. Defaults to false to enforce the
    reproducibility of the trajectory
[use_barostat = <bool>]
    apply an MC-like barostat to the simulation
[P = <float>]
    the pressure of the simulation
[delta_L = <float>]
    controls the box side change by the MC-like barostat
backend = CPU
    For CPU FFS
backend_precision = <any>
    CPU FFS may use any precision allowed for a normal CPU MD simulation
sim_type = FFS_MD
    This must be set for an FFS simulation
newtonian_steps = <int>
    number of integration timesteps after which the thermostat acts. Can
    be 1.
pt = <float>
    probability of refreshing the momenta of each particle
diff_coeff = <float>
    base diffusion coefficient. Either pt or diff_coeff should be
    specified in the input file
gamma_trans = <float>
    translational damping coefficient for the Langevin thermostat. Either
    this or diff_coeff should be specified in the input file.
bussi_tau = <int>
    correlation time, in time steps, for the stochastic evolution of the
    kinetic energy
DPD_zeta = <float>
    translational damping coefficient for the DPD thermostat.
[thermostat = no|refresh|brownian|langevin|srd]
    Select the simulation thermostat for MD simulations. 'no' means
    constant-energy simulations. 'refresh' is the Anderson thermostat.
    'brownian' is an Anderson-like thermostat that refreshes momenta of
    randomly chosen particles. 'langevin' implements a regular Langevin
    thermostat. 'srd' is an (experimental) implementation of a stochastic
    rotational dynamics algorithm. 'no' and 'brownian' are also available
    on CUDA. Defaults to 'no'.

MC options:

ensemble = nvt|npt
    ensemble of the simulation
[check_energy_every = <float>]
    oxDNA will compute the energy from scratch, compare it with the
    current energy and throw an error if the difference is larger then
    check_energy_threshold. Defaults to 10.
[check_energy_threshold = <float>]
    threshold for the energy check. Defaults to 1e-2f for single precision
    and 1e-6 for double precision.
delta_translation = <float>
    controls the trial translational displacement, which is a randomly
    chosen number between -0.5*delta and 0.5*delta for each direction.
delta_rotation = <float>
    controls the angular rotational displacement, given by a randomly
    chosen angle between -0.5*delta and 0.5*delta radians.
delta_volume = <float>
    controls the volume change in npt simulations.
P = <float>
    the pressure of the simulation. Used only if ensemble == npt.
[adjust_moves = <bool>]
    if true, oxDNA will run for equilibration_steps time steps while
    changing the delta of the moves in order to have an optimal acceptance
    ratio. It does not make sense if equilibration_steps is 0 or not
    given. Defaults to false
[maxclust = <int>]
    Default: N; maximum number of particles to be moved together. Defaults
    to the whole system
[small_system = <bool>]
    Default: false; whether to use an interaction computation suited for
    small systems.
[preserve_topology = <bool>]
    Default: false; sets a maximum size for the move attempt to 0.5, which
    guarantees that the topology of the system is conserved. Also prevents
    very large moves and might speed up simulations of larger systems,
    while suppressing diffusion
[umbrella_sampling = <bool>]
    Default: false; whether to use umbrella sampling
[op_file = <string>]
    Mandatory if umbrella_sampling is set to true; path to file with the
    description of the order parameter
[weights_file = <string>]
    Mandatory if umbrella_sampling is set to true; path to file with the
    weights to use in umbrella sampling
[last_hist_file = <string>]
    Optional if umbrella_sampling is set to true, otherwise ignored;
    Default: last_hist.dat; path to file where the histograms associated
    with umbrella sampling will be stored. This is printed with the same
    frequency as the energy file. Should become an observable sooner or
    later
[traj_hist_file = <string>]
    Optional if umbrella_sampling is set to true, otherwise ignored;
    Default: traj_hist.dat; path to file where the series histograms
    associated with umbrella sampling will be stored, allowing to monitor
    the time evolution of the histogram and possibly to remove parts of
    the simulation. This is printed with the same frequency as the energy
    file. Should become an observable sooner or later
[init_hist_file = <string>]
    Optional if umbrella_sampling is set to true, otherwise ignored;
    Default: none; path to a file to load a previous histogram from,
    useful if one wants to continue a simulation to obtain more
    statistics.
[extrapolate_hist = <float>,<float>,..., <float>]
    Optional if umbrella_sampling is set to true, otherwise ignored;
    Default: none; series of temperatures to which to extrapolate the
    histograms. They can be given as float in reduced units, or the units
    can be specified as in the T option
[safe_weights = <bool>]
    Default: true; whether to check consistency in between order parameter
    file and weight file. Only used if umbrella_sampling = true
[default_weight = <float>]
    Default: none; mandatory if safe_weights = true; default weight for
    states that have no specified weight assigned from the weights file
[skip_hist_zeros = <bool>]
    Default: false; Wether to skip zero entries in the traj_hist file
[equilibration_steps = <int>]
    Default: 0; number of steps to ignore to allow for equilibration
[type = rotation|traslation|possibly other as they get added]
    move to perform. No Defaults

Interactions/DNA2Interaction.h options:

salt_concentration = <float>
    sets the salt concentration in M
[dh_lambda = <float>]
    the value that lambda, which is a function of temperature (T) and salt
    concentration (I), should take when T=300K and I=1M, defaults to the
    value from Debye-Huckel theory, 0.3616455
[dh_strength = <float>]
    the value that scales the overall strength of the Debye-Huckel
    interaction, defaults to 0.0543
[dh_half_charged_ends = <bool>]
    set to false for 2N charges for an N-base-pair duplex, defaults to 1

Interactions/DHSInteraction.h options:

DHS_eps = <float>
    background dielectrci constant for reaction field treatment
DHS_rcut = <float>
    cutoff for the reaction field treatment

Interactions/DNAInteraction.h options:

[use_average_seq = <boolean>]
    defaults to yes
[hb_multiplier = <float>]
    HB interaction multiplier applied to all the nucleotides having a
    custom numbered base whose magnitude is > 300, defaults to 1.0
[max_backbone_force = <float>]
    defaults to nothing, has to be > 0) (if set to a float value, it
    specifies the maximum force (in reduced units) that the FENE bonds
    will exert. After the separation corresponding to the specified value,
    the potential has a form A x + B log(x), where A and B are computed
    automatically to obtain a continuous, differentiable and monotonically
    increasing potential. The computation involves the value of
    max_backbone_force as well as the value of max_backbone_force_far,
    below
[max_backbone_force_far = <float>]
    defaults to 0.04, only read if max_backbone_force is set, has to be >
    0) (limit value of the force exerted by the bonded interactions for
    large separations, in reduced units. Used in the computation of A and
    B above. The default value is set to be very weak (0.04 = ~2pN), so
    that two neighbours will eventually get close without ever breaking
    base pairs

Interactions/KFInteraction.h options:

KF_N = <int>
    number of patches
KF_continuous = <bool>
    selects either the original KF model, valid only for MC simulations,
    or its continuous variant (see ACS Nano 10, 5459 (2016))
KF_delta = <float>
    radial width of the patches
KF_cosmax = <float>
    angular half-width of the patches
[KF_N_B = <int>]
    number of patches on species B
[KF_epsilon_AA = <float>]
    depth of the well of the patch-patch interaction between particles of
    species A
[KF_epsilon_BB = <float>]
    depth of the well of the patch-patch interaction between particles of
    species B
[KF_epsilon_AB = <float>]
    depth of the well of the patch-patch interaction between particles of
    unlike species
[KF_sigma_AA = <float>]
    diameter controlling the repulsive interaction between particles of
    species A
[KF_sigma_BB = <float>]
    diameter controlling the repulsive interaction between particles of
    species B
[KF_sigma_AB = <float>]
    diameter controlling the repulsive interaction between particles of
    unlike species

Interactions/PatchyInteraction.h options:

PATCHY_N = <int>
    number of patches
[PATCHY_N_B = <int>]
    number of patches on species B
[PATCHY_alpha = <float>]
    width of patches, defaults to 0.12
[PATCHY_epsilon_AA = <float>]
    depth of the well of the patch-patch interaction between particles of
    species A
[PATCHY_epsilon_BB = <float>]
    depth of the well of the patch-patch interaction between particles of
    species B
[PATCHY_epsilon_AB = <float>]
    depth of the well of the patch-patch interaction between particles of
    different species
[PATCHY_sigma_AA = <float>]
    diameter controlling the repulsive interaction between particles of
    species A
[PATCHY_sigma_BB = <float>]
    diameter controlling the repulsive interaction between particles of
    species B
[PATCHY_sigma_AB = <float>]
    diameter controlling the repulsive interaction between particles of
    different species

Interactions/BoxInteraction.h options:

box_sides = <float>, <float>, <float>
    sides of the box

Interactions/TSPInteraction.h options:

TSP_rfene = <float>
    FENE length constant for bonded interactions
TSP_sigma[type] = <float>
    particle diameter associated to each interaction
TSP_epsilon[type] = <float>
    energy scale associated to each interaction
TSP_attractive[type] = <float>
    whether the interaction contains an attractive tail or not
TSP_n[type] = <int>
    exponent for the generalised LJ potential for each interaction
[TSP_attractive_anchor = <bool>]
    set to true if you want the anchor monomer to be of type B instead of
    type A. Defaults to false
[TSP_only_chains = <bool>]
    if true the system will be composed of chains only. The topology will
    be interpreted accordingly by ignoring the first value of each line
    (which, in the case of TSPs, is the number of arms). Defaults to false
[TSP_only_intra = <bool>]
    if true monomers belonging to different stars will not interact.
    Defaults to false

Interactions/HardSpheroCylinderInteraction.h options:

length = <float>
    length of the spherocylinder

Interactions/InteractionFactory.h options:

[interaction_type = DNA|RNA|HS|LJ|patchy|patchyDan|TSP|DNA_relax|DNA_nomesh|Box|HardCylinder|HardSpheroCylinder|DHS|Dirk]
    Particle-particle interaction of choice. Check the documentation
    relative to the specific interaction for more details. Defaults to
    dna.

Interactions/JordanInteraction.h options:

JORDAN_N_patches = <int>
    number of patches
[JORDAN_s = <float>]
    sigma of the gaussian modulation, defaults to 0.3
[JORDAN_m = <float>]
    exponent to the 2m-m lennard-jones part
[JORDAN_phi = <float>]
    angle below the equator for the rest position of the patches, defaults
    to PI/6
[JORDAN_int_k = <float>]
    stiffness of the internal spring, defaults to 0., i.e., free patches

Interactions/RNAInteraction.h options:

[use_average_seq = <boolean>]
    defaults to yes
[seq_dep_file = <string>]
    sets the location of the files with sequence-dependent parameters
[external_model = <string>]
    overrides default constants for the model, set in rna_model.h), by
    values specified by this option

Interactions/LJInteraction.h options:

LJ_rcut = <float>
    interaction cutoff
[LJ_kob_andersen = <bool>]
    Simulate a Kob-Andersen mixture. Defaults to false.
[LJ_n = <int>]
    Generalised LJ exponent. Defaults to 6, which is the classic LJ value.

Interactions/RNAInteraction2.h options:

[use_average_seq = <boolean>]
    defaults to yes
[seq_dep_file = <string>]
    sets the location of the files with sequence-dependent parameters
[external_model = <string>]
    overrides default constants for the model, set in rna_model.h), by
    values specified by this option
[salt = <float>]
    sets the salt concentration in M, defaults to 1
[mismatch_repulsion = <boolean>]
    defaults to no
[mismatch_repulsion_strength = <float>]
    defaults to 1, sets the strength of repulsion if mismatch_repulsion is
    true

Interactions/HardCylinderInteraction.h options:

height = <float>
    cylinder length

Interactions/TEPInteraction.h options:

[_prefer_harmonic_over_fene = <bool>]
    if True, neighbouring beads are bound by an harmonic potential instead
    of a FENE one. Defaults to false.
[_allow_broken_fene = <bool>]
    if True, the code won't die when the beads are beyond the acceptable
    FENE range. Defaults to True.

Interactions/DNAInteraction_relax.h options:

relax_type = <string>
    Possible values: constant_force, harmonic_force; Relaxation algorithm
    used
relax_strength = <float>
    Force constant for the replacement of the FENE potential

Interactions/DNAInteraction_relax2.h options:

relax_type = <string>
    Possible values: constant_force, harmonic_force; Relaxation algorithm
    used
relax_strength = <float>
    Force constant for the replacement of the FENE potential

Interactions/RNAInteraction_relax.h options:

relax_type = <string>
    Possible values: constant_force, harmonic_force; Relaxation algorithm
    used
relax_strength = <float>
    Force constant for the replacement of the FENE potential

CUDA options:

[CUDA_list = no|verlet]
    Neighbour lists for CUDA simulations. Defaults to 'no'.
backend = CUDA
    For CUDA FFS -- NB unlike the CPU implementation, the CUDA
    implementation does not print extra columns with the current order
    parameter values whenever the energy is printed
backend_precision = mixed
    CUDA FFS is currently only implemented for mixed precision
sim_type = FFS_MD
    This must be set for an FFS simulation
order_parameters_file = <string>
    path to the order parameters file
ffs_file = <string>
    path to the file with the simulation stopping conditions. Optionally,
    one may use 'master conditions' (CUDA FFS only), which allow one to
    more easily handle very high dimensional order parameters. See the
    EXAMPLES/CUDA_FFS/README file for more information
[ffs_generate_flux = <bool>]
    CUDA FFS only. Default: False; if False, the simulation will run until
    a stopping condition is reached; if True, a flux generation simulation
    will be run, in which case reaching a condition will cause a
    configuration to be saved but will not terminate the simulation. In
    the stopping condition file, the conditions must be labelled forward1,
    forward2, ... (for the forward conditions); and backward1, backward2,
    ... (for the backward conditions), ... instead of condition1,
    condition2, ... . To get standard flux generation, set the forward and
    backward conditions to correspond to crossing the same interface (and
    use conditions corresponding to different interfaces for Tom's flux
    generation). As with the single shooting run mode, the name of the
    condition crossed will be printed to stderr each time.
[gen_flux_save_every = <integer>]
    CUDA FFS only. Mandatory if ffs_generate_flux is True; save a
    configuration for 1 in every N forward crossings
[gen_flux_total_crossings = <integer>]
    CUDA FFS only. Mandatory if ffs_generate_flux is True; stop the
    simulation after N crossings achieved
[gen_flux_conf_prefix = <string>]
    CUDA FFS only. Mandatory if ffs_generate_flux is True; the prefix used
    for the file names of configurations corresponding to the saved
    forward crossings. Counting starts at zero so the 3rd crossing
    configuration will be saved as MY_PREFIX_N2.dat
[gen_flux_debug = <bool>]
    CUDA FFS only. Default: False; In a flux generation simulation, set to
    true to save backward-crossing configurations for debugging
[check_initial_state = <bool>]
    CUDA FFS only. Default: False; in a flux generation simulation, set to
    true to turn on initial state checking. In this mode an initial
    configuration that crosses the forward conditions after only 1 step
    will cause the code to complain and exit. Useful for checking that a
    flux generation simulation does not start out of the A-state
[die_on_unexpected_master = <bool>]
    CUDA FFS only. Default: False; in a flux generation simulation that
    uses master conditions, set to true to cause the simulation to die if
    any master conditions except master_forward1 or master_backward1 are
    reached. Useful for checking that a flux generation simulation does
    not enter any unwanted free energy basins (i.e. other than the initial
    state and the desired final state)
[unexpected_master_prefix = <string>]
    CUDA FFS only. Mandatory if die_on_unexpected_master is True; the
    prefix used for the file names of configurations corresponding to
    reaching any unexpected master conditions (see
    die_on_unexpected_master).
[CUDA_device = <int>]
    CUDA-enabled device to run the simulation on. If it is not specified
    or it is given a negative number, a suitable device will be
    automatically chosen.
[CUDA_sort_every = <int>]
    sort particles according to a 3D Hilbert curve every CUDA_sort_every
    time steps. This will greatly enhnance performances for some types of
    interaction. Defaults to 0, which disables sorting.
[threads_per_block = <int>]
    Number of threads per block on the CUDA grid. defaults to 2 * the size
    of a warp.

Analysis options:

[analysis_confs_to_skip = <int>]
    number of configurations that should be excluded from the analysis.
analysis_data_output_<n> = {
ObservableOutput
}
    specify an analysis output stream. <n> is an integer number and should
    start from 1. The setup and usage of output streams are documented in
    the ObservableOutput class.

Observables/HBEnergy.h options:

[pairs_file = <string>]
    OrderParameter file containing the list of pairs whose HB energy is to
    be computed
[base_file = <string>]
    file containing a list of nucleotides whose HB energy is to be
    computed, one nucleotide per line

Observables/ParticlePosition.h options:

particle_id = <int>
    particle id
[orientation = <bool>]
    defaults to false. If 1, it also prints out the orientation
[absolute = <bool>]
    defaults to false. If 1, does not use periodic boundaries and it
    prints out the absolute position of the center of mass

Observables/StretchedBonds.h options:

print_list = <bool>
    Whether to print the indexes of the particles that have stretched
    bonds. If set to false, only the total number of streched bonds is
    printed. Defaults to true
[threshold = <float>]
    Threshold above which to report a stretched bond, in energy units.
    Default is 1.

Observables/VectorAngle.h options:

[first_particle_index = <int>]
    defaults to 0. index of the first particle on which to compute the
    angle with the next particle.
[last_particle_index = <int>]
    defaults to the index of the first-but last bead in the same strand as
    the first particle. Therefore, if I have a strand of N beads, the last
    one will be the one with index N-2. This is because the last bead is
    atypical in the TEP model (e.g. it's aligned with the vector before it
    rather than the one in front of it.). index of the last particle of
    the chain on which to compute the angle.
[angle_index = <int>]
    defaults to 1. Can be 1,2, or 3 depending on which orientation vector
    we want to compute the cosine, or 0. In that case it measures the
    amount of twist, defined as in the TEP model: (1 +
    v2.v2'+v3.v3')/(2*pi)*(1 + v1.v1') where v1, v2 and v3 are the
    orientation vectors of the first particle in a pair and v1', v2' and
    v3' are the orientation vectors of the following particle.
[print_local_details = <bool>]
    defaults to true. If true, print the quantity relative to each pair of
    particles. Otherwise, print their average (for angle_index == 1,2,3)
    OR their sum (that is, the total twist, for angle_index = 0.

Observables/Step.h options:

[units = steps|MD]
    units to print the time on. time in MD units = steps * dt, defaults to
    step

Observables/Pressure.h options:

type = pressure
    an observable that computes the osmotic pressure of the system
[stress_tensor = <bool>]
    if true, the output will contain 9 fields: the total pressure and the
    nine components of the stress tensor, xx, xy, xz, yx, yy, yz, zx, zy,
    zz

Observables/Pitch.h options:

bp1a_id = <int>
    base pair 1 particle a id
bp1b_id = <int>
    base pair 1 particle b id
bp2a_id = <int>
    base pair 2 particle a id
bp2b_id = <int>
    base pair 2 particle b id

Observables/SaltExtrapolation.h options:

salts = <float>, <float>, ...
    list of salt concentration to extrapolate to
temps = <T>, <T>, ...
    list of temperatures to extrapolate to, separated with commas.
    Temperatures can be specified in reduced units, Kelvin, Celsius as
    0.10105, 30C, 30c, 30 c, 303.15 k, 303.15K, 303.15k
[op_file = <string>]
    order parameter file. If not found, it will use the one from the input
    file
[weights_file = <string>]
    weights file. If not found, the one from the input file will be used.

Observables/Distance.h options:

particle_1 = <int>
    index of the first particle or comma-separated list of particle
    indexes composing the first set
particle_2 = <int>
    index of the second particle or comma-separated list of the particle
    indexes composing the second set. The distance is returned as r(2) -
    r(1)
[PBC = <bool>]
    Whether to honour PBC. Defaults to True
[dir = <float>, <float>, <float>]
    vector to project the distance along. Beware that it gets normalized
    after reading. Defaults to (1, 1, 1) / sqrt(3)

Observables/TEPPlectonemePosition.h options:

[bead_minimum_distance = <int>]
    the minimum integer separation between beads whose relative distance
    will be checked. Defaults to 7
[distance_threshold = <float>]
    a plectoneme is identified when any two beads with indices farther
    away than bead_minimum_distance are closer than this distance.
    Defaults to 2

Observables/MeanVectorCosine.h options:

chain_id = <int>
    chain id
first_particle_position = <int>
    defaults to 0. position along the chain of  the first particle on
    which to compute the vector's cosine with the next particle
last_particle_position = <int>
    defaults to N-2, where N is the number of elements of the chain.
    Position along the chain of the last particle over which to compute
    the vector's cosine with the next particle
vector_to_average = <int>
    defaults to 1. Can be 1,2, or 3 depending on the vectors we wish to
    consider, or 0. In that case it measures the quantity (v2*v2')(v3*v3')
    - |v2 ^ v2||v3 ^ v3|

Observables/PotentialEnergy.h options:

[split = <bool>]
    defaults to false, it tells the observable to print all the terms
    contributing to the potential energy

Observables/Writhe.h options:

[first_particle_index = <int>]
    defaults to 0. index of the first particle on which to compute the
    angle with the next particle.
[last_particle_index = <int>]
    defaults to the index of the first-but last bead in the same strand as
    the first particle. Therefore, if I have a strand of N beads, the last
    one will be the one with index N-2. This is because the last bead is
    atypical in the TEP model (e.g. it's aligned with the vector before it
    rather than the one in front of it.). index of the last particle of
    the chain on which to compute the angle.
[subdomain_size = <int>]
    if locate_plectonemes is false, defaults to the entire subchain,
    therefore computing the total writhe,otherwise it defaults to 35. If
    smaller, the writhe will be computed only on the beads between i and
    i+subdomain_size, for every i between first_particle_index and
    last_particle_index (wrapping around if go_round is true, or not
    computing it if the end of the chain is reached otherwise.
[go_around = <bool>]
    whether to assume periodic boundary conditions when building
    subdomains - see above. Defaults to true if the last particle is right
    before the first and if subdomain_size is not the entire subchain, and
    to false otherwise.
[locate_plectonemes = <bool>]
    if this is true, the writhe will be used to locate plectonemes with
    the algorithm from Vologodskii et al. "Conformational and
    THermodynamic Properties of Supercoiled DNA (1992)" and the indices on
    beads at the center of a plectoneme loop will be printed. Defaults to
    false.
[writhe_threshold = <double>]
    if the writhe exceeds this, then we mark a plectoneme. Only used if
    locate_plectonemes is true. Defaults to 0.28, since this is the value
    that works best with a subdomain_size of 35, which is the default one.
[print_space_position = <bool>]
    defaults to false. Whether to print the position of the plectoneme tip
    segment in 3d space as well as its index. Only used if
    locate_plectonemes = true.
[print_size = <bool>]
    defaults to false. Whether to print the plectoneme size compute with
    Ferdinando-Lorenzo's algorithm. Only used if locate_plectonemes =
    true.
[contact_threshold = <number>]
    defaults to 5. Segments closer than this will be considered to be
    touching accourding to the plectoneme size algorithm.
[size_outer_threshold = <int>]
    defaults to 30. Outer threshold parameter, which substantially is the
    maximum separation in indices between two points of contact of a
    plectoneme loop, for the plectoneme size algorithm.
[minimum_plectoneme_size = <int>]
    defaults to 1. Plectonemes shorter than this wont' be reported.
[bending_angle_number_segments = <int>]
    defaults to 0. When non-zero, the angle between that many segments
    surrounding the plectoneme tip will be averaged and printed on file.

Observables/CoaxVariables.h options:

particle1_id = <int>
    particle 1 id
particle2_id = <int>
    particle 2 id

Observables/ForceEnergy.h options:

[print_group = <string>]
    limits the energy computation to the forces belonging to a specific
    group of forces. This can be set by adding a group_name option to each
    force's input. By default ForceEnergy computes the energy due to all
    the forces.

Observables/PairEnergy.h options:

particle1_id = <int>
    particle 1 id
particle2_id = <int>
    particle 2 id

Observables/StructureFactor.h options:

max_q = <float>
    maximum q to consider
[type = <int>]
    particle species to consider. Defaults to -1, which means "all
    particles"

Observables/DensityProfile.h options:

max_value = <float>
    anything with a relevant coordinate grater than this will be ignored.
    Mind that the observable is PBC-aware.
bin_size = <float>
    the bin size for the profile
axis = <char>
    Possible values: x, y, z the axis along which to compute the profile

Observables/Contacts.h options:

[first_particle_index = <int>]
    defaults to 0. index of the first particle to consider. All the
    particles coming before this one will be ignored.
[last_particle_index = <int>]
    defaults to the index of the first-but last bead in the same strand as
    the first particle. Therefore, if I have a strand of N beads, the last
    one will be the one with index N-2. This is because the last bead is
    atypical in the TEP model (e.g. it's aligned with the vector before it
    rather than the one in front of it.). index of the last particle to
    consider. All the particles coming before this one will be ignored.
[neighbours_to_ignore = <int>]
    defalts to 1. Number of neighbours to ignore before-after each
    particle. E.g., if equals to 1, contacts between given first-
    neighbours will never be reported, if equals to 2, contacts between
    second neighbours will never be reported, etc.
[contact_distance = <number>]
    defaults to 1. A contact is defined if the centers of mass of the
    particles is lower than this value.
[only_outermost_contacts = <bool>]
    defaults to false. if true, contacts nested within other contacts will
    not be reported. E.g. if the i-th monomer is linked to both the i-1-th
    and the i+1-th monomer, and the contacts are 10-40, 10-25, 13-32,
    12-48 and 45-60, only 10-40, 12-48 and 45-60 will be reported, since
    10-25 and 13-32 are both nested inside 10-40. This is only get one
    result per plectoneme. Whatch out though, since this will report
    clashes between a plectoneme and the chain/other plectonemes. Telling
    a plectoneme and a plectoneme contact just by using the contact map
    might be non-banal.

Observables/PairForce.h options:

[particle_id = <int>]
    Optional argument. particle id.

Observables/ObservableOutput.h options:

name = <string>
    name of the output stream. stdout or stderr are accepted values
print_every = <integer>
    frequency of output, in number steps for oxDNA, in number of
    configurations for DNAnalysis
[start_from = <integer>]
    start outputing from the given step, defaults to 0
[stop_at = <integer>]
    stop outputing at this step, defaults to -1 (which means never)
[only_last = <bool>]
    if true, the output will not be appended to the stream, but it will
    overwrite the previous output each time, defaults to false
[binary = <bool>]
    if true, the output will be printed in binary, defaults to false
[linear = <bool>]
    if true the OutputObservable will save in linear scale, otherwise will
    use the logline scale by FS. Defaults to true
[update_name_with_time = <bool>]
    if true the output filename will be changed by using the 'name' key as
    a prefix and the current step as a suffix. Defaults to false
col_<n> = {
type = name of the first observable
[other observable options as lines of 'key = value']
}
    this syntax specifies the column of the output file. Note that <n> is
    the column index and should start from 1

Observables/Rdf.h options:

max_value = <float>
    maximum r to consider
bin_size = <float>
    bin size for the g(r)
[axes = <string>]
    Possible values: x, y, z, xy, yx, zy, yz, xz, zx. Those are the axes
    to consider in the computation. Mind that the normalization always
    assumes 3D sytems for the time being.

Observables/HBList.h options:

type = hb_list
    name of  the observable
only_count = <bool>
    if True, don't report the detailed binding profile but just count the
    bonds. Defaults to False.

Observables/Configurations/TEPtclOutput.h options:

[back_in_box = <bool>]
    Default: true; if true the particle positions will be brought back in
    the box
[show = <int>,<int>,...]
    Default: all particles; list of comma-separated indexes of the
    particles that will be shown. Other particles will not appear
[hide = <int>,<int>,...]
    Default: no particles; list of comma-separated indexes of particles
    that will not be shown
[print_labels = <bool>]
    Default: false; if true labels with the strand id are printed next to
    one end of the strand.
[resolution = <int>]
    Default: 20; resolution set in the tcl file.
[ref_particle = <int>]
    Default: -1, no action; The particle with the id specified (starting
    from 0) is set at the centre of the box. Overriden if ref_strands is
    specified. Ignored if negative or too large for the system.
[ref_strand = <int>]
    Default: -1, no action; The strand with the id specified, starting
    from 1, is set at the centre of the box. Ignored if negative or too
    large for the system.

Observables/Configurations/TEPxyzOutput.h options:

[back_in_box = <bool>]
    Default: true; if true the particle positions will be brought back in
    the box
[show = <int>,<int>,...]
    Default: all particles; list of comma-separated indexes of the
    particles that will be shown. Other particles will not appear
[hide = <int>,<int>,...]
    Default: no particles; list of comma-separated indexes of particles
    that will not be shown
[ref_particle = <int>]
    Default: -1, no action; The particle with the id specified (starting
    from 0) is set at the centre of the box. Overriden if ref_strands is
    specified. Ignored if negative or too large for the system.
[ref_strand = <int>]
    Default: -1, no action; The strand with the id specified, starting
    from 1, is set at the centre of the box. Ignored if negative or too
    large for the system.

Observables/Configurations/Configuration.h options:

[back_in_box = <bool>]
    if true the particle positions will be brought back in the box,
    defaults to false
[show = <int>,<int>,...]
    list of comma-separated particle indexes whose positions will be put
    into the final configuration
[hide = <int>,<int>,...]
    list of comma-separated particle indexes whose positions won't be put
    into the final configuration
[reduced = <bool>]
    if true only the strand centres of mass will be printed, defaults to
    false

Observables/Configurations/PdbOutput.h options:

[back_in_box = <bool>]
    Default: true; if true the particle positions will be brought back in
    the box
[show = <int>,<int>,...]
    Default: all particles; list of comma-separated indexes of the
    particles that will be shown. Other particles will not appear
[hide = <int>,<int>,...]
    Default: no particles; list of comma-separated indexes of particles
    that will not be shown
[ref_particle = <int>]
    Default: -1, no action; The nucleotide with the id specified (starting
    from 0) is set at the centre of the box. Overriden if ref_strands is
    specified. Ignored if negative or too large for the system.
[ref_strand = <int>]
    Default: -1, no action; The strand with the id specified (starts from
    1) is set at the centre of the box. Ignored if negative or too large
    for the system.

Observables/Configurations/ChimeraOutput.h options:

[colour_by_sequece = <bool>]
    Default: false; whether to coulour the bases according to the base
    type (A, C, G, T

Observables/Configurations/TclOutput.h options:

[back_in_box = <bool>]
    Default: true; if true the particle positions will be brought back in
    the box
[show = <int>,<int>,...]
    Default: all particles; list of comma-separated indexes of the
    particles that will be shown. Other particles will not appear
[hide = <int>,<int>,...]
    Default: no particles; list of comma-separated indexes of particles
    that will not be shown
[print_labels = <bool>]
    Default: false; if true labels with the strand id are printed next to
    one end of the strand.
[resolution = <int>]
    Default: 20; resolution set in the tcl file.
[ref_particle = <int>]
    Default: -1, no action; The nucleotide with the id specified (starting
    from 0) is set at the centre of the box. Overriden if ref_strands is
    specified. Ignored if negative or too large for the system.
[ref_strand = <int>]
    Default: -1, no action; The strand with the id specified, starting
    from 1, is set at the centre of the box. Ignored if negative or too
    large for the system.

Forces/COMForce.h options:

stiff = <float>
    stiffness of the spring
r0 = <float>
    equilibrium elongation of the spring
com_list = <string>
    comma-separated list containing the ids of all the particles whose
    centre of mass is subject to the force
ref_list = <string>
    comma-separated list containing the ids of all the particles whose
    centre of mass is the reference point for the force acting on the
    other group of particles

Forces/RepulsionPlane.h options:

stiff = <float>
    stiffness of the repulsion.
dir = <float>,<float>,<float>
    the vector normal to the plane: it should point towards the half-plane
    where the repulsion is not acting.
position = <float>
    defines the position of the plane along the direction identified by
    the plane normal.
particle = <int>
    index of the particle on which the force shall be applied. If -1, the
    force will be exerted on all the particles.

Forces/LJWall.h options:

dir = <float>,<float>,<float>
    the vector normal to the plane: it should point towards the half-plane
    where the repulsion is not acting.
position = <float>
    defines the position of the plane along the direction identified by
    the plane normal.
particle = <int>
    index of the particle on which the force shall be applied. If -1, the
    force will be exerted on all the particles.
[stiff = <float>]
    stiffness of the repulsion. Defaults to 1.
[sigma = <float>]
    "Diameter" of the wall. It effectively rescales the distance between
    particle and wall. Defaults to 1.
[n = <int>]
    Exponent of the 2n-n generalized Lennard-Jones expression. Defaults to
    6.
[only_repulsive = <bool>]
    If true, the interactio between particle and wall gets cut-off at the
    minimum, resulting in a purely-repulsive potential. Defaults to false.
[generate_inside = <bool>]
    If true the wall-particle interaction may not diverge, even for
    negative distances. Useful when generating the starting configuration.
    Defaults to false

Forces/GenericCentralForce.h options:

particle = <int>
    comma-separated list of indices of particles to apply the force to. -1
    applies it to all particles. Entries separated by a dash "-" get
    expanded in a list of all the particles on a same strand comprised
    between the two indices. E.g., particle= 1,2,5-7 applies the force to
    1,2,5,6,7 if 5 and 7 are on the same strand.
center = <float>,<float>,<float>
    the centre from which the force originates from

Forces/ConstantRateForce.h options:

particle = <int>
    comma-separated list of indices of particles to apply the force to. -1
    applies it to all particles. Entries separated by a dash "-" get
    expanded in a list of all the particles on a same strand comprised
    between the two indices. E.g., particle= 1,2,5-7 applies the force to
    1,2,5,6,7 if 5 and 7 are on the same strand.
F0 = <float>
    Initial force.
rate = <float>
    growth rate of the force. It is [oxDNA energy units / (oxDNA distance
    units * (MD/MC) steps].
[dir_as_centre = <bool>]
    if true the "dir" parameter will be interpreted as the origin of the
    force, so that the true direction will be dir - p->pos

Forces/RepulsiveSphere.h options:

stiff = <float>
    stiffness of the repulsion.
r0 = <float>
    radius of the sphere, in simulation units.
rate = <float>
    rate of growth of the radius. Note that the growth is linear in
    timesteps/MC steps, not reduced time units.
particle = <int>
    index of the particle on which the force shall be applied. If -1, the
    force will be exerted on all the particles
[center = <float>,<float>,<float>]
    centre of the sphere, defaults to 0,0,0

Forces/SawtoothForce.h options:

particle = <int>
    particle to apply the force to. -1 applies it to all particles.
F0 = <float>
    Initial force
wait_time = <float>
    time interval over which the force is constant. Units are (MD/MC)
    steps.
increment = <float>
    amount by which to increment the force every wait_time steps.

Forces/RepulsionPlaneMoving.h options:

stiff = <float>
    stiffness of the repulsion.
dir = <float>,<float>,<float>
    the vector normal to the plane: it should point towards the half-plane
    where the repulsion is not acting.
particle = <int>
    index(es) of the particle(s) on which the force shall be applied. Can
    be a list of comma-separated indexes. If -1, the force will be exerted
    on all the particles.
ref_particle = <int>
    index(es) of the particle(s) whose position along the normal will be
    used to define the repulsive plane(s). Can be a list of comma-
    separated indexes.

Forces/HardWall.h options:

dir = <float>,<float>,<float>
    the vector normal to the plane: it should point towards the half-plane
    that is allowed to the particles.
position = <float>
    defines the position of the plane along the direction identified by
    the plane normal.
particle = <int>
    index of the particle on which the force shall be applied. If -1, the
    force will be exerted on all the particles.
[sigma = <float>]
    "Diameter" of the wall. It effectively rescales the distance between
    particle and wall. Defaults to 1.

Forward Flux Sampling (FFS) options:

backend = CPU/CUDA
    For CPU FFS/For CUDA FFS -- NB unlike the CPU implementation, the CUDA
    implementation does not print extra columns with the current order
    parameter values whenever the energy is printed
backend_precision = <any>/mixed
    CPU FFS may use any precision allowed for a normal CPU MD
    simulation/CUDA FFS is currently only implemented for mixed precision
sim_type = FFS_MD
    This must be set for an FFS simulation
order_parameters_file = <string>
    path to the order parameters file
ffs_file = <string>
    path to the file with the simulation stopping conditions. Optionally,
    one may use 'master conditions' (CUDA FFS only), which allow one to
    more easily handle very high dimensional order parameters. See the
    EXAMPLES/CUDA_FFS/README file for more information
[ffs_generate_flux = <bool>]
    CUDA FFS only. Default: False; if False, the simulation will run until
    a stopping condition is reached; if True, a flux generation simulation
    will be run, in which case reaching a condition will cause a
    configuration to be saved but will not terminate the simulation. In
    the stopping condition file, the conditions must be labelled forward1,
    forward2, ... (for the forward conditions); and backward1, backward2,
    ... (for the backward conditions), ... instead of condition1,
    condition2, ... . To get standard flux generation, set the forward and
    backward conditions to correspond to crossing the same interface (and
    use conditions corresponding to different interfaces for Tom's flux
    generation). As with the single shooting run mode, the name of the
    condition crossed will be printed to stderr each time.
[gen_flux_save_every = <integer>]
    CUDA FFS only. Mandatory if ffs_generate_flux is True; save a
    configuration for 1 in every N forward crossings
[gen_flux_total_crossings = <integer>]
    CUDA FFS only. Mandatory if ffs_generate_flux is True; stop the
    simulation after N crossings achieved
[gen_flux_conf_prefix = <string>]
    CUDA FFS only. Mandatory if ffs_generate_flux is True; the prefix used
    for the file names of configurations corresponding to the saved
    forward crossings. Counting starts at zero so the 3rd crossing
    configuration will be saved as MY_PREFIX_N2.dat
[gen_flux_debug = <bool>]
    CUDA FFS only. Default: False; In a flux generation simulation, set to
    true to save backward-crossing configurations for debugging
[check_initial_state = <bool>]
    CUDA FFS only. Default: False; in a flux generation simulation, set to
    true to turn on initial state checking. In this mode an initial
    configuration that crosses the forward conditions after only 1 step
    will cause the code to complain and exit. Useful for checking that a
    flux generation simulation does not start out of the A-state
[die_on_unexpected_master = <bool>]
    CUDA FFS only. Default: False; in a flux generation simulation that
    uses master conditions, set to true to cause the simulation to die if
    any master conditions except master_forward1 or master_backward1 are
    reached. Useful for checking that a flux generation simulation does
    not enter any unwanted free energy basins (i.e. other than the initial
    state and the desired final state)
[unexpected_master_prefix = <string>]
    CUDA FFS only. Mandatory if die_on_unexpected_master is True; the
    prefix used for the file names of configurations corresponding to
    reaching any unexpected master conditions (see
    die_on_unexpected_master).