Rovigattil: Created page with "===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 simulat…"

2014-03-19T11:25:37Z

Created page with "===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 simulat…"

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===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 ([[DNA_model_introduction|oxDNA model]]) is the default option. RNA ([[RNA_model_introduction|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|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.

Input options of the previous version - Revision history

Rovigattil: Created page with "===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 simulat…"