Input options of the previous version

Generic options

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

[interaction_type = DNA]

DNA|RNA|patchy|LJ

(selects the model for the simulation. DNA (oxDNA model) is the default option. RNA (oxRNA model), LJ (Lennard-Jones) and patchy particles are also implemented

[sim_type=MD]

MD|MC

MD = Molecular Dynamics, MC = Monte Carlo

backend

CPU | CUDA

(only sim_type=MD is supported if you choose CUDA backend)

backend_precision

float|double|mixed

(mixed option is available only for CUDA backend. It is recommended choice for optimal performance on CUDA machines, double is recommended for CPU simulations)

[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; if 1, the step counter will be reset to 0. The total duration of the simulation is unchanged.

[seed=time(NULL)]

seed for the random number generator. On Unix systems, 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 somewhat misleading: the actual verlet skin is 2*verlet_skin.

[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). Make sure you read thermostat.

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.