Observables

The observable infrastructure was devised to help building customized output from oxDNA (and DNAnalysis) without having to dive in the simulation code itself.

The relevant keys in the input file are analysis_data_output_* (used by DNAnalysis) and data_output_* (used by oxDNA). These take as an argument, between curly brackets, a series of lines that is interpreted as an input file and whose options dictate the way the resulting output file is printed.

Warning

data_output_i (with i integer) will not be taken into consideration if all data_output_j for j < i are present. The same holds true for analysis_data_output_*.

The following options are supported:

name: the name of the output file. If stdout or stderr than the standard output or the standard error will be used, respectively. Mandatory.
linear: if set to “true” then the output will be printed every print_every time steps. If set to “false” a log-linear scale will be used instead, where the output will be printed in linearly-spaced cycles made of log-spaced times. More specifically, the \(i\)-th output time will be given by \(t_i = t_{jp} + n_0 (i - jp)^k\), where \(p\) is the number of points per cycle, \(j = \lfloor i / p\rfloor\) and \(n_0\) and \(k\) are additional parameters. Defaults to true.
print_every: the number of time steps every which the output is written. Mandatory if linear = true.
log_ppc: The number of points per cycle, \(p\). Mandatory if linear = false.
log_n0: The parameter \(n_0\). Mandatory if linear = false.
log_fact: The parameter \(k\). Mandatory if linear = false.
col_*: an option that expects text enclosed by curly brackets that specifies the observable to be printed in the given column *. Note that col_i requires that all col_j with j < i are also present.
start_from: the number of steps beyond which the output will be written. Defaults to 0.
stop_at: the number of steps beyond which the output will stop being written. Defaults to -1 (“never”).
only_last: overwrite the content of the output with the current one.
update_name_with_time: change the name of the output file every time the output is printed by appending the current simulation time step to name.

An example is:

data_output_1 = {
	name = prova.dat
	print_every = 100
	col_1 = {
		type = step
		units = MD
	}
	col_2 = {
		type = potential_energy
	}
}

this will print in prova.dat two colums, the first with the steps in MD units (dt-aware) and the second with the potential energy.

Note

oxDNA provides a plugin infrastructure to manage additional Observables. See the doxygen documentation for src/PluginManagement/PluginManager.h. The contrib folder contains a few working plugins you can use as starting points to write your owns.

External observable file

Output files and observables can also be specified in an external JSON file by setting the non-mandatory option observables_file in the main input file. The following snippet shows an example of such a file:

{
  "output_1" : {
    "print_every" : "10000",
    "name" : "hb_energy.dat",
    "cols" : [
      {
        "type" : "step",
        "units" : "MD"
      },
      {
        "type" : "hb_energy"
      }
    ]
  },
  "output_2" : {
    "print_every" : "1000",
    "name" : "pot_energy.dat",
    "cols" : [
      {
        "type" : "step"
      },
      {
        "type" : "potential_energy"
      }
    ]
  }
}

Common options

The following options are supported by all observabes:

[id = <string>]: a unique identifier that can be used to refer to this specific observable (see e.g. get_observable_by_id()).
[update_every = <int>]: the number of time steps every which the observable is updated (but no output is printed). Note that this is supported only by some observables.

Simulation time

Print the current simulation time as the number of steps or as molecular-dynamics time.

type = step: the observable type.
[units = steps|MD]: units to print the time on. The time in MD units is defined as steps * dt. Defaults to step.

Total potential energy

Print the total potential energy of the system.

type = potential_energy: the observable type.
[split = <bool>]: print all the terms contributing to the potential energy. Defaults to false.

Hydrogen-bonding energy

Compute and print the hydrogen-bonding (HB) energy of all or selected nucleotides or of selected pairs of nucleotides. By default the observable computes and prints the total HB energy.

type = hb_energy: the observable type.
[pairs_file = <path>]: an order parameter file containing the list of pairs whose total HB energy is to be computed.
[bases_file = <path>]: file containing a list of nucleotides whose total HB energy is to be computed, one nucleotide per line. If both this option and pairs_file are set, the former is silently ignored.

Hydrogen bonds

Compute and print the hydrogen bonds (the detailed bonding pattern or, optionally, only their total number) that are present in all the system or, optionally, between specific pairs.

type = hb_list: the observable type.
[order_parameters_file = <path>]: an order parameter file containing the list of pairs that should be checked for HB bonds.
[only_count = <bool>]: if true, don’t report the detailed binding profile but just count the bonds. Defaults to false.

Position of a single nucleotide

Print the position and, optionally, the orientation of a specific nucleotide.

type = particle_position: the observable type.
particle_id = <int>: the particle id.
[orientation = <bool>]: if true the observable also prints out the \(\vec{a}_1\) and \(\vec{a}_3\) orientation vectors (see here for details). Defaults to false.
[absolute = <bool>]: if true the observable does not apply periodic boundaries and it prints out the absolute position of the center of mass of the nucleotide. Defaults to false.

Forces and torques due to pair interactions

Print forces and torques due to nucleotide-nucleotide interactions. By default, all interacting pairs are printed.

type = pair_force: the observable type.
[particle_id = <int>]: if set, only pairs in which one of the particles has the given id will be considered.

Distance between two (sets of) particles

Print the euclidean distance between two particles or between the centres of mass of two sets of particles.

type = distance: the observable type.
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 \(|\vec{r}_2 - \vec{r}_1|\).
[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 \((1, 1, 1) / \sqrt{3}\).

Distance between all pairs of particles

Print the distance between all particle pairs. Nota Bene: this observable prints all \(N^2\) distances, where \(N\) is the number of nucleotides in the simulation.

type = contact_map: the observable type.

Interaction energy between pairs of particles

Print the pair interaction energy between all pairs formed by particles that are close enough to interact or between two specific particles. Note that the output interaction energy is split into its contributions. For oxDNA1 these are the backbone, bonded excluded volume, stacking, non-bonded excluded volume, hydrogen bonding, cross stacking and coaxial stacking. For oxDNA2 there is also a Debye-Hueckel contribution.

type = pair_energy: the observable type.
[particle1_id = <int>]: particle 1 id. If not set, the observable will print the interaction energy between all pairs, defined as two particles that are close enough to feel each other.
[particle2_id = <int>]: particle 2 id. Used only if particle1_id is set.

Stretched bonds

Print the list (or, optionally, only the number) of stretched bonds present in the system. A stretched bond is defined as a bond whose associated energy exceeds a given threshold.

type = stretched: the observable type.
[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. Defaults to 1.

Energy associated to the external forces

Print the energy associated to all (or a subset of) the external forces acting on the nucleotides.

type = force_energy: the observable type.
[print_group = <string>]: limit the energy computation to the forces belonging to a specific group of forces. This can be set by adding a group_name option to the desired external forces. If not set, all external forces will be considered.

External force acting on particle(s)

Print the force vector acting on all (or a subset of all) particles due to external forces. This observable supports the update_every option.

type = external_force: the observable type.
particles: list of comma-separated particle indexes whose force vectors should be printed.

Configuration

Print an oxDNA configuration.

Note

This observable can be used to save disk space by generating trajectories containing only those nucleotides that are of interest (i.e. whose positions, orientations and possibly momenta are required for post-processing). The following example will generate a trajectory with configurations spaced by 1000 time steps containing the positions and orientations (but not the momenta) of the first 5 nucleotides only:

data_output_1 = {
	name = traj_small.dat
	print_every = 1000
	col_1 = {
		type = configuration
		show = 0,1,2,3,4
		print_momenta = false
	}
}

type = configuration: the observable type.
[print_momenta = <bool>]: print the linear and angular momenta of the particles to the trajectory. Set it to false to decrease the size of the trajectory by \(\approx 40\%\). Defaults to true.
[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. If not set, all particles will be printed.
[hide = <int>,<int>,...]: list of comma-separated particle indexes whose positions won’t be put into the final configuration. If not set, no particles will be hidden.
[reduced = <bool>]: if true only the centres of mass of the strands will be printed. Defaults to false.

Pressure

Compute the osmotic pressure of the system.

type = pressure: the observable type.
[stress_tensor = <bool>]: if true, the output will contain 7 fields: the total pressure and 6 components of the (symmetric) stress tensor: \(xx, yy, zz, xy, xz, yz\). Defaults to false
[PV_only = <bool>]: if true, the pressure and (optionally) the stress tensor won’t be divided by the volume of the simulation box. Defaults to false.

Stress autocorrelation

Compute the stress autocorrelation function \(G(t)\) using the multi-tau method describere here. This observable supports the update_every option.

[m = <int>]: size of the average used by the algorithm. Defaults to 2.
[p = <int>]: The size of the coarse-grained levels used by the algorithm. Defaults to 16.
[serialise = <bool>]: if true, every time the observable is printed, also generate files that can be used to recreate the observable’s data structures. This makes it possible to restart simulations that keep accumulating statistics for the autocorrelation. Note that if this is set to true, then the observable will look for these files to reload the data upon restarting. Defaults to false.

Pitch

type = pitch: the observable type
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.

Structure factor

This observable supports the update_every option.

type = Sq: the observable type.
max_q = <float>: maximum wave vector \(q\) to consider.
[type = <int>]: particle species to consider. Defaults to -1, which means “all particles”

Density profile

type = density_profile: the observable type.
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>: the axis along which to compute the profile. Possible values are x, y, or z.

Radial distribution function

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

Vector angle

TEP interaction only.

type = vector_angle: the observable type.
[first_particle_index = <int>]: index of the first particle on which to compute the angle with the next particle. Defaults to 0.
[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>]: 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’)/(2pi)(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. Defaults to 1.
[print_local_details = <bool>]: 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). Defaults to true.

Writhe

TEP interaction only.

type = writhe: the observable type.
[first_particle_index = <int>]: index of the first particle on which to compute the angle with the next particle. Defaults to 0.
[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 set to 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 = 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 computed 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.

TEP contacts

TEP interaction only.

type = contacts: the observable type.
[first_particle_index = <int>]: index of the first particle to consider. All the particles coming before this one will be ignored. Defaults to 0.
[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>]: 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. Defalts to 1.
[contact_distance = <number>]: A contact is defined if the centers of mass of the particles is lower than this value. Defaults to 1.
[only_outermost_contacts = <bool>]: 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. Watch 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-trivial. Defaults to false.

Observables

External observable file

Common options

Simulation time

Total potential energy

Hydrogen-bonding energy

Hydrogen bonds

Position of a single nucleotide

Forces and torques due to pair interactions

Distance between two (sets of) particles

Distance between all pairs of particles

Interaction energy between pairs of particles

Stretched bonds

Energy associated to the external forces

External force acting on particle(s)

Configuration

Pressure

Stress autocorrelation

Pitch

Coaxial-stacking-related quantities

Structure factor

Density profile

Radial distribution function

Vector angle

Writhe

TEP contacts