Input options

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

[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.

[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.

verlet_skin = <float>

width of the skin that controls the maximum displacement after which Verlet lists need to be updated.

name = stream name

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

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

MD options

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

[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'.

newtonian_steps = <int>

number of integration timesteps after which momenta are refreshed

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.

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

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

Interactions/DHSInteraction.h options

DHS_eps = <float>

background dielectrci constant for reaction field treatment

DHS_rcut = <float>

cutoff for the reaction field treatment

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/DirkInteraction2.h options

length = <float>

lenght of the cylinders

DHS_radius = <float>

radius of the diploar hard sphere on top of each cylinder

DHS_rcut = <float>

distance cutoff for the reaction field treatment

DHS_eps = <float>

background dielectric constant for the reaction field treatment

Interactions/InteractionFactory.h options

[interaction_type = DNA|RNA|HS|LJ|patchy|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/HardSpheroCylinderInteraction.h options

length = <float>

length of the spherocylinder

Interactions/BoxInteraction.h options

box_sides = <float>, <float>, <float>

sides of the box

Interactions/DirkInteraction.h options

length = <float>

lenght of the cylinders

DHS_radius = <float>

radius of the diploar hard sphere on top of each cylinder

DHS_rcut = <float>

distance cutoff for the reaction field treatment

DHS_eps = <float>

background dielectric constant for the reaction field treatment

Interactions/LJInteraction.h options

LJ_rcut = <float>

interaction cutoff

[LJ_kob_andersen = <bool>]

Simulate a Kob-Andersen mixture. Defaults to false.

Interactions/HardCylinderInteraction.h options

height = <float>

cylinder length

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/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

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

CUDA options

[CUDA_list = no|verlet]

Neighbour lists for CUDA simulations. Defaults to 'no'.

[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.

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).

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/Step.h options

[units = steps|MD]

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

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/Pressure.h options

type = pressure

an observable that computes the osmotic pressure of the system

[stress_tensor = <bool>]

if true, the output will contain 7 fields, with the first being the total pressure and the other 6 the six independent components of the stress tensor, xx, yy, zz, xy, xz, yz

Observables/CoaxVariables.h options

particle1_id = <int>

particle 1 id

particle2_id = <int>

particle 2 id

Observables/PotentialEnergy.h options

[split = <bool>]

defaults to false, it tells the observable to print all the terms contributing to the potential energy

Observables/ObservableOutput.h options

name = stream name

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

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/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/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/Distance.h options

particle_1 = <int>

index of the first particle

particle_2 = <int>

index of the second particle. 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/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/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.

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

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).