oxDNA README
------------
oxDNA is a simulation code that was initially conceived as an implementation of the coarse-grained DNA
model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis (http://dx.doi.org/10.1063/1.3552946).
It has been since reworked and it is now an extensible simulation+analysis framework.
It natively supports DNA, RNA, Lennard-Jones and patchy particle simulations on both CPU and NVIDIA
GPUs.
The development of this software has been partially supported by the European Commission through the Marie
Skłodowska−Curie Fellowship No. 702298-DELTAS.
REQUIREMENTS
------------
Without CUDA support:
cmake >= 2.6
make
gcc >= 4.2 / icc >= 11.0
With CUDA support:
cmake >= 2.8
make
gcc >= 4.2 / icc >= 11.0
CUDA toolkit >= 4.0
Generating the documentation (with 'make docs', see below) requires doxygen.
COMPILING oxDNA
---------------
Extract the oxDNA archive and then:
cd oxDNA # enter the oxDNA folder
mkdir build # create a new build folder. It is good practice to compile out-of-source
cd build
cmake .. # here you can specify additional options, see next section
make -j4 # compile oxDNA. The -jX make option makes it compile the code in parallel by using X threads.
At the end of the compilation three executables (oxDNA, DNAnalysis and confGenerator) will be placed
in the build/bin folder.
CMAKE OPTIONS
-------------
-DCUDA=ON Enables CUDA support
-DCUDA_COMMON_ARCH=ON Choose the target CUDA compute architecture based on the nvcc version. Set it to off to autodetect the CUDA compute arch GPU installed.
-DDebug=ON Compiles with debug symbols and without optimisation flags
-DG=ON Compiles with debug symbols + optimisation flags
-DINTEL=ON Uses INTEL's compiler suite
-DMPI=ON Compiles oxDNA with MPI support
-DCXX11=ON Compiles oxDNA with c++11 support
-DSIGNAL=OFF Handling system signals is not always supported. Set this flag to OFF to remove this feature
-DMOSIX=ON Makes oxDNA compatible with MOSIX
MAKE TARGETS
-------------
make
Compiles oxDNA
make docs
Produces html doxygen documentation.
oxDNA: DOCS/html_oxDNA/index.html
UTILS: DOCS/html_UTILS/index.html
make rovigatti
Compiles the observables and interactions in contrib/rovigatti
make romano
Compiles the observables and interactions in contrib/romano
TESTING
-------
make test_run
Runs quick tests to check whether oxDNA has been correctly compiled or not.
make test_quick
Runs longer tests to check that oxDNA works (not fully implemented yet, but the main features are supported).
USAGE
-----
oxDNA input_file
OUTPUT FILE
-----------
The energy.dat (default name, can be changed in the configuration file) has this layout for MD:
time potential_energy kinetic_energy total_energy
The energy.dat (default name, can be changed in the configuration file) has this layout for MC:
time potential_energy hydrogen_bonding_energy acc_trasl acc_rot [acc_volume]
Mind that potential, kinetic and total energies are divided by the number of particles.
Configurations are saved in the trajectory file (appended one after the other).
OBSERVABLES
-----------
The observable infrastructure was devised to help building
customized output from oxDNA (and DNAAnalysis) without having to
dive in the simulation code itself.
The relevant keys in the input file are analysis_data_output_* and
data_output_* (see below). These take as an argument, between curly
brackets, a series of lines that is interpreted as an input file.
An example is:
data_output_1 = {
name = caca.dat
print_every = 100
col_1 = {
type = potential_energy
}
col_2 = {
type = step
units = MD
}
}
this will print in caca.dat two colums, the first with the
potential energy and the second with the steps in MD units (dt
aware).
The lines in between curly brackets are interpreted as input files
by the single observables.
See also the doxygen documentation for Observables/ObservableOutput.h
oxDNA provides a plugin infrastructure to manage additional
Observables. See the doxygen documentation for PluginManagement/PluginManager.h
INPUT FILE OPTIONS
------------------
As always in UNIX environments, everything is case sensitive.
The options are in the form key = value. Key-value pairs should be either on different
lines or separated by a semicolon. There can be arbitrary spaces before and after both key and value.
Line with a leading # will be treated as comments. The expected type of the value is specified between < and >.
A <bool> 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).
-------------------------------------------------------------------------------
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.
[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.
-------------------------------------------------------------------------------
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.
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'.
bussi_tau = <int>
correlation time, in time steps, for the stochastic evolution of the
kinetic energy
-------------------------------------------------------------------------------
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/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/HardCylinderInteraction.h options:
height = <float>
cylinder length
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/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/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/DHSInteraction.h options:
DHS_eps = <float>
background dielectrci constant for reaction field treatment
DHS_rcut = <float>
cutoff for the reaction field treatment
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
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/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/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/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/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/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/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/BoxInteraction.h options:
box_sides = <float>, <float>, <float>
sides of the box
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
-------------------------------------------------------------------------------
CUDA options:
[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).
[CUDA_list = no|verlet]
Neighbour lists for CUDA simulations. Defaults to 'no'.
-------------------------------------------------------------------------------
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/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.
measure_mean_shift = <bool>
if True, measure the mean absolute shift in base-pair register, as
described below. Defaults to false.
max_shift = 5
with this option, we compute the distances between each unpaired base
and a domain of length 2*_max_shift+1 bases on the other strand,
centred on the base in complementary position. The absolute
topological displacement between the closes base and the complementary
base is then reported: for example, if an unpaired base is actually
closest to a base that is 3 basepairs ahead of its complementary
basepair, its shift will be 3, assuming that max_shift (see below) is
3 or more. The threshold is supposed to prevent accounting for
plectoneme loops, so shouldn't be too much, but should also ultimately
be greater than most values measured.
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/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/PairForce.h options:
[particle_id = <int>]
Optional argument. particle id.
Observables/AverageEnergy.h options:
type = average_energy
name of the observable
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/PotentialEnergy.h options:
[split = <bool>]
defaults to false, it tells the observable to print all the terms
contributing to the potential energy
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/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/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/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.
[print_left_right = <bool>]
defaults to false. Does everything like with the print_size option,
but instead of printing the sizes it prints the indices of the first
and last bead/base-pair of the plectoneme. Can't be used together with
print_size. 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/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/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/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/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/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/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/StructureFactor.h options:
max_q = <float>
maximum q to consider
[type = <int>]
particle species to consider. Defaults to -1, which means "all
particles"
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/CoaxVariables.h options:
particle1_id = <int>
particle 1 id
particle2_id = <int>
particle 2 id
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/Step.h options:
[units = steps|MD]
units to print the time on. time in MD units = steps * dt, defaults to
step
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/PairEnergy.h options:
particle1_id = <int>
particle 1 id
particle2_id = <int>
particle 2 id
print_header = <bool>
if true, print a header that explains the value of each column, and a
newline after the list of particles. defaults to true
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/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/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/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/RepulsiveSphereSmooth.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/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/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/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/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/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/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.
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/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/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
-------------------------------------------------------------------------------
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).
-------------------------------------------------------------------------------
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