Documentation

Compile options

Compiling oxDNA requires that you change the first rows in the makefile to match your machine configuration. The following parameters can be passed to make:

• dbg=1 oxDNA will be compiled with debug flags (both for nvcc and gcc). The resulting executable will be put in the Debug directory.
• g=1 oxDNA will be compiled with both debug and optimization flags. The resulting executable will be put in the Release directory.
• intel=1 oxDNA will be compiled using the Intel icpc compiler. The resulting executable will be named oxDNA_intel.

Usage

oxDNA input_file

Input file

As always in UNIX environments, everything is case sensitive. The options are in the form key = value. There can be arbitrary spaces before and after both key and value. Line with a leading # will be treated as comments. In this part | (pipe) is the separator between the different values that can be used to specify a value for the key. Keys between [ and ] are optional, the value after the equal sign is the default value.

Generic options

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

[sim_type=MD]

MD|MC

MD = Molecular Dynamics, MC = Monte Carlo

backend

CPU

backend_precision

float|double

[debug=0]

0|1

1 if you want verbose logs, 0 otherwise.

Simulation options

The options listed here specify the behaviour of the simulation.

steps

number of steps to be performed.

[restart_step_counter=0]

0|1

0 means that the step counter will start from the value read in the configuration file, 1 otherwise.

[seed=time(NULL)

seed for the random number generator. On Unix systesm, it will use by default a number from /dev/urandom + time(NULL)

T

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).

Examples:

Value	Simulation Units
0.1	0.1
300 K	0.1
300k	0.1
26.85c	0.1
26.85 C	0.1

verlet_skin

if a particle moves more than verlet_skin then the lists will be updated. Its name is misleading: the actual verlet skin is 2*verlet_skin. I'm sorry for that :)

[use_average_seq=1]

0|1

specifies whether to use the default hard-coded average parameters for base-pairing and stacking interaction strengths or not. If sequence dependence is to be used, set this to 0 and specify seq_dep_file.

[seq_dep_file]

specifies the file from which the sequence dependent parameters should be read. Mandatory if use_average_seq=no, ignored otherwise. A sample file is provided (sequence_dependent_parameters.txt).

[external_forces=0]

0|1

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]

specifies the file containing all the external forces' configurations. Currently there are six supported force types (see EXAMPLES/TRAPS for some examples):

• string
• twist
• trap
• repulsion_plane
• repulsion_plane_moving
• mutual_trap

Molecular dynamics simulations options

dt

time step of the integration.

thermostat

no|refresh|john

no means no thermostat will be used. refresh will refresh all the particle's velocities from a maxwellian every newtonian_steps steps. john is an Anderson-like thermostat (see pt).

newtonian_steps

required if thermostat != no

number of steps after which a procedure of thermalization will be performed.

pt

used if thermostat == john. It's the probability that a particle's velocity will be refreshed during a thermalization procedure.

diff_coeff

required if pt is not specified

used internally to automatically compute the pt that would be needed if we wanted such a self diffusion coefficient. Not used if pt is set.

Monte Carlo simulations options

[check_energy_every=10]

this number times print_energy_every gives the number of steps after which the energy will be computed from scratch and checked against the actual value computed adding energy differences.

[check_energy_threshold=1e-4]

if abs((old_energy - new_energy)/old_energy) > check_energy_threshold then the program will die and warn the user.

ensemble

NVT

ensemble of the simulation. More ensembles could be added in future versions.

delta_translation

maximum displacement (per dimension) for translational moves in simulation units.

delta_translation

maximum displacement for rotational moves in simulation units.

Input/output

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

conf_file

initial configuration file.

topology

file containing the system's topology.

trajectory_file

the main output of the program. All the configurations will be appended to this file as they are printed.

[confs_to_skip=0]

valid only if conf_file is a trajectory. Skip the first confs_to_skip configurations and then load in memory the (confs_to_skip+1)th.

[lastconf_file=last_conf.dat]

this is the file where the last configuration is saved (when the program finishes or is killed). Set to last_conf.dat by default

[refresh_vel=0]

0|1

if 1 the initial velocities will be refreshed from a maxwellian.

energy_file

energy output file.

[print_energy_every=1000]

this will make the program print the energies every print_energy_every steps.

[no_stdout_energy=0]

0|1

if 1 the energy will be printed just to the energy_file.

[time_scale=linear]

linear|log_lin

using linear configurations will be saved every print_conf_interval.

using log_lin configurations will be saved logarithmically for print_conf_ppc times. After that the logarithmic sequence will restart.

print_conf_interval

linear interval if time_scale == linear. First step of the logarithmic scale if time_scale == log_lin.

print_conf_ppc

used if time_scale == log_lin

points per logarithmic cycle.

[print_reduced_conf_every=0]

every print_reduced_conf_every steps the program will print out the reduced configurations (i.e. confs containing only the centers of mass of strands).

reduced_conf_output_dir

used if print_reduced_conf_every > 0

output directory for reduced_conf files.

[log_file=stderr]

file where generic and debug informations will be logged. If not specified then stderr will be used.

[print_timings=0]

0|1

if 1 the MD step timing have be printed to a file.

timings_filename

used if print_timings == 1

output file where the MD step timing will be appended to.

Output files

• The log file contains all relevant informations about the simulation (specified options, activated external forces, warnings about misconfiguratios, critical errors, etc.). If the log file is omitted, all these informations will be displayed on the standard output.

• The energy file layout for MD simulations is

time

potential energy

kinetic energy

total energy

hydrogen bonding energy

while for MC simulations is

time

potential energy

hydrogen bonding energy

acceptance ratio for translational moves

acceptance ratio for rotational moves

Mind that potential, kinetic and total energies are divided by the number of particles whereas the hydrogen bonding energy is not.

• Configurations are saved in the trajectory file.