OxDNA - User contributions [en]

Thermostat

2013-03-19T16:06:36Z

Romano:

The best thermostat implemented in the simulation code (''john'' thermostat) is a simple thermostat
that emulates Brownian dynamics. The system is evolved integrating Newton's
equations of motion ('NVE' ensemble) for a given (small) number of steps.
Then the velocity and momentum of each particle are refreshed, with a given
fixed probability. The new velocities and momenta are chosen according to
the Maxwell distribution of the temperature at which the simulation is run.
This approximates a Brownian dynamics on time scales much longer than the
refresh interval.

* '''dt''' time steps of the integration
* '''newtonian steps''' number of steps between refresh attempts
* '''pt''' the probability with which each particle gets its velocity and momentum refreshed at each attempt.
* '''diff_coeff''' the overall monomer diffusion coefficient resulting from the thermostat. The code internally sets <tt>pt</tt> to get this value. Specifying <tt>pt</tt> will override this, regardless which comes first in the input file.

The algorithm works as follows: the system is evolved for a number of steps equal to <tt>newtonian_steps</tt> according to Newton's equations of motion. Then for each particle a random number is extracted; if it is larger than the value for <tt>pt</tt> (either set explicitly or derived
from <tt>diff_coeff</tt>) the particle is left untouched. If the random number extracted is lower than the value of <tt>pt</tt>, each of the components of the the velocity and angular momentum of the particle are refreshed according to
the Maxwell distribution dictated by the value of the temperature.

A completely Brownian dynamics (on the time scale set by <tt>dt</tt>) can be obtained setting <tt>pt = 1</tt> and <tt>newtonian_steps = 0</tt>. Of course, this makes little sense.

Increasing the value of <tt>pt</tt> makes the dynamics more dumped, so that overall diffusion is slower but local motion is somewhat better explored. We found that a good thermostat setting to study diffusion-limited events is to set <tt>diff_coeff = 2.5</tt> and <tt>newtonian_steps = 103</tt>. If one is not limited by diffusion, internal relaxation can be speeded up by lowering the value of <tt>diff_coeff</tt> by a factor 2 or 4.

Publications

2013-02-25T12:00:28Z

Romano:

#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''Phys. Rev. Lett''. '''104''', 178101 (2010)
#:[http://prl.aps.org/abstract/PRL/v104/i17/e178101 DNA Nanotweezers Studied with a Coarse-Grained Model of DNA] ([http://arxiv.org/abs/0911.0555 arXiv])
#T. E. Ouldridge, A. A. Louis and J. P. K. Doye, ''J. Chem. Phys'', '''134''', 085101 (2011)
#:[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])
#T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
#:[http://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719 Coarse-grained modelling of DNA and DNA self-assembly]
#F. Romano, A. Hudson, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, ''J. Chem. Phys.'' '''136''', 215102 (2012)
#:[http://jcp.aip.org/resource/1/jcpsa6/v136/i21/p215102_s1 The effect of topology on the structure and free energy landscape of DNA kissing complexes] ([http://arxiv.org/abs/1203.3577 arXiv])
#C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, ''Soft Matter'' '''8''', 8388 (2012)
#:[http://pubs.rsc.org/en/content/articlelanding/2012/sm/c2sm25845e Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link] ([http://arxiv.org/abs/1204.0985 arXiv])
#C. Matek, T. E. Ouldridge, A. Levy, J. P. K. Doye, A. A. Louis, ''J. Phys. Chem. B'' (2012)
#:[http://pubs.acs.org/doi/abs/10.1021/jp3080755 DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism] ([http://arxiv.org/abs/1206.2636 arXiv])
#P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
#:[http://jcp.aip.org/resource/1/jcpsa6/v137/i13/p135101_s1 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])
#F. Romano, D. Chakraborty, J. P. K. Doye, T. E. Ouldridge, A. A. Louis, ''J. Chem. Phys.'' '''138''', 085101 (2013)
#:[http://jcp.aip.org/resource/1/jcpsa6/v138/i8/p085101_s1 Coarse-grained simulations of DNA overstretching] ([http://arxiv.org/abs/1209.5892 arXiv])
#P. Šulc, T. E. Ouldridge, F. Romano, J. P. K. Doye, A. A. Louis, "arxiv" (2012)
#:[http://arxiv.org/abs/1212.4536 Simulating a burnt-bridges DNA motor with a coarse-grained DNA model]
#T. E. Ouldridge, R. L. Hoare, A. A. Louis, J. P. K. Doye, J. Bath, A. J. Turberfield, ''ACS Nano'' (2013)
#:[http://pubs.acs.org/doi/abs/10.1021/nn3058483 Optimizing DNA nanotechnology through coarse-grained modelling: a two-footed DNA walker]

Publications

2013-02-25T11:55:42Z

Romano:

Model introduction

2012-12-12T11:35:55Z

Romano: /* Simulation units */

The model treats DNA as a string of rigid nucleotides, which interact through potentials which depend on the position and orientation of the nucleotides. The interactions are:
#Sugar-phosphate backbone connectivity,
#Excluded volume,
#Hydrogen bonding,
#Nearest-neighbour stacking,
#Cross-stacking between base-pair steps in a duplex,
#Coaxial stacking.

This interactions are illustrated below. Orientational modulations of the stacking potential encourage the bases to form coplanar stacks, the twist arising from the different length scales of the backbone separation and the optimum stacking separation. The possibility of unstacking allows single strands to be very flexible. Hydrogen bonding can occur between complementary bases when they are anti-aligned, leading to the formation of double helical structures.

http://www-thphys.physics.ox.ac.uk/people/ThomasOuldridge/Site/The_model.png

(a) Model interaction sites with their interaction ranges (the typical range of an interaction is twice the radius of the sphere shown).

(b) Representation of these interaction site in a visualisation that makes the planarity of the base clear.

(c) A duplex in this representation.

http://www-thphys.physics.ox.ac.uk/people/ThomasOuldridge/Site/interactions.png

Indication of the interactions which hold together a typical duplex. V(b.b.) indicates the phosphate-sugar backbone connectivity.

In the original model, all complementary base pairs and stacking partners interact with the same strength (there is no attractive interaction between non-complementary bases). A sequence-dependent parameterisation of the hydrogen-bonding and stacking interactions is included as an option in the code release.
The melting temperatures of a set of short DNA oligomers in the sequence-dependent coarse-grained model, compared to the melting temperatures as predicted by SantaLucia's nearest-neighbor model ([http://www.pnas.org/content/95/4/1460.full]), are available here: [http://www-thphys.physics.ox.ac.uk/people/PetrSulc/data/CG_model_Tm.txt]

The model does not incorporate the differentiation between the major and minor grooves of DNA double helices, and incorporates electrostatics only through the short-ranged excluded volume. For this reason, it is only appropriate for the study of systems at high salt concentration, when electrostatic interactions are strongly screened.

===Simulation units===
The code uses dimensionless energy, mass, length and timescales for convenience. The relationship between simulation units (SU) and SI units is given below.

{|
|-
! Simulation unit
! Physical unit
|-
| 1 unit of length
| 8.518x10<math>^{-10}</math> m
|-
| 1 unit of energy
| 4.142x10<math>^{-20}</math> J
|-
| 1 unit of temperature
| 3000 K
|-
| 1 unit of force
| 4.863x10<math>^{-11}</math> N
|-
| 1 unit of mass
| 1.66x10<math>^{-25}</math> kg
|-
| 1 unit of time
| 1.71x10<math>^{-12}</math> s
|-
|}

The model and its performance is discussed in detail in the following references (the thesis provides the most complete analysis):

T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
[http://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719 Coarse-grained modelling of DNA and DNA self-assembly]

T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)
[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])

P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
[http://jcp.aip.org/resource/1/jcpsa6/v137/i13/p135101_s1 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])

Model introduction

2012-12-12T11:35:29Z

Romano: /* Simulation units */

The model treats DNA as a string of rigid nucleotides, which interact through potentials which depend on the position and orientation of the nucleotides. The interactions are:
#Sugar-phosphate backbone connectivity,
#Excluded volume,
#Hydrogen bonding,
#Nearest-neighbour stacking,
#Cross-stacking between base-pair steps in a duplex,
#Coaxial stacking.

This interactions are illustrated below. Orientational modulations of the stacking potential encourage the bases to form coplanar stacks, the twist arising from the different length scales of the backbone separation and the optimum stacking separation. The possibility of unstacking allows single strands to be very flexible. Hydrogen bonding can occur between complementary bases when they are anti-aligned, leading to the formation of double helical structures.

http://www-thphys.physics.ox.ac.uk/people/ThomasOuldridge/Site/The_model.png

(a) Model interaction sites with their interaction ranges (the typical range of an interaction is twice the radius of the sphere shown).

(b) Representation of these interaction site in a visualisation that makes the planarity of the base clear.

(c) A duplex in this representation.

http://www-thphys.physics.ox.ac.uk/people/ThomasOuldridge/Site/interactions.png

Indication of the interactions which hold together a typical duplex. V(b.b.) indicates the phosphate-sugar backbone connectivity.

In the original model, all complementary base pairs and stacking partners interact with the same strength (there is no attractive interaction between non-complementary bases). A sequence-dependent parameterisation of the hydrogen-bonding and stacking interactions is included as an option in the code release.
The melting temperatures of a set of short DNA oligomers in the sequence-dependent coarse-grained model, compared to the melting temperatures as predicted by SantaLucia's nearest-neighbor model ([http://www.pnas.org/content/95/4/1460.full]), are available here: [http://www-thphys.physics.ox.ac.uk/people/PetrSulc/data/CG_model_Tm.txt]

The model does not incorporate the differentiation between the major and minor grooves of DNA double helices, and incorporates electrostatics only through the short-ranged excluded volume. For this reason, it is only appropriate for the study of systems at high salt concentration, when electrostatic interactions are strongly screened.

===Simulation units===
The code uses dimensionless energy, mass, length and timescales for convenience. The relationship between simulation units (SU) and SI units is given below.

{|
|-
! Simulation unit
! Physical unit
|-
| 1 unit of length
| 8.518x10<math>^{-10}</math> m
|-
| 1 unit of energy
| 4.142x10<math>^{-20}</math> J
|-
| 1 unit of Temperature
| 3000 K
|-
| 1 unit of Force
| 4.863x10<math>^{-11}</math> N
|-
| 1 unit of Mass
| 1.66x10<math>^{-25}</math> kg
|-
| 1 unit of Time
| 1.71x10<math>^{-12}</math> s
|-
|}

The model and its performance is discussed in detail in the following references (the thesis provides the most complete analysis):

T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
[http://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719 Coarse-grained modelling of DNA and DNA self-assembly]

T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)
[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])

P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
[http://jcp.aip.org/resource/1/jcpsa6/v137/i13/p135101_s1 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])

Screenshots and movies

2012-11-08T16:59:49Z

Romano:

=== single-stranded DNA ===
[[Image:image_ssdna.png]]

=== double-stranded DNA ===
[[Image:image_dsdna.png]]

=== DNA tetrahedron ===
http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/image.png

=== Strand displacement ===
http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/stateB.png
Invading strand attached by toehold

http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/stateC.png
Invading and victim strands that are not coaxially stacked

http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/stateX.png
Invading and victim strands that are coaxially stacked

http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/movie2.mp4 A movie of part of the strand displacement process. It shows the invading strand attached by toehold and then displacing several base pairs of the victim strand

=== DX tile ===
http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/tilechimera.png

=== Kissing hairpin ===
[[Image:hairpin_kiss2.png]]

File:Image dsdna.png

2012-11-08T16:58:02Z

Romano:

2012-09-24T14:00:13Z

Romano:

==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==

<pre>oxDNA input_file</pre>

The input file contains all the relevant information for the program to run, such as what initial configuration to use, the topology of the system, how often to print the energies to a file, etc. Please make sure you read the [[Thermostat|thermostat]] page if you use molecular dynamics.

==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; 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.

==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.

==Configuration and topology files==
The current state of a system, as by oxDNA, is described by two files: a configuration file and a topology file. The configuration file contains all the general informations (timestep, energy and box size) and orientations and positions of each nucleotide. The topology file, on the other hand, keeps track of the backbone-backbone bonds between nucleotides in the same strand. Working configuration and topology files can be found in the <tt>[[Examples|EXAMPLES]]</tt> directory.

===Configuration file===
The first three rows of a configuration file contain the timestep <tt>T</tt> at which the configuration has been printed, the length of the box sides <tt>Lx</tt>, <tt>Ly</tt> and <tt>Lz</tt> and the total, potential and kinetic energies, <tt>Etot</tt>, <tt>U</tt> and <tt>K</tt>, respectively:

<pre>
t = T
b = Lz Ly Lz
E = Etot U K
</pre>

after this header, each row contains position of the centre of mass, orientation, velocity and angular velocity of a single nucleotide in the following order:

<math>\overbrace{r_x r_y r_z}^{\rm Position} \overbrace{b_x b_y b_z}^{\rm Backbone-base versor} \overbrace{n_x n_y n_z}^{\rm Normal versor} \overbrace{v_x v_y v_z}^{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular velocity}</math>

===Topology file===
The topology file stores the intra-strand, fixed bonding topology (i.e. which nucleotides share backbone links). The first row contains the total number of nucleotides <tt>N</tt> and the number of strands <tt>Ns</tt>:

<pre>
N Ns
</pre>

After this header, the <tt>i</tt>-th row specifies strand, base and 3' and 5' neighbors of the <tt>i</tt>-th nucleotide in this way:

<pre>
S B 3' 5'
</pre>

where S is the number of the strand (starting from 1) which the nucleotide belongs to, B is the base and 3' and 5' specify the index of the nucleotides with which the <tt>i</tt>-th nucleotide is bonded in the 3' and 5' direction, respectively. A <tt>-1</tt> signals that the nucleotide terminates the strand in either 3' or 5' direction. The topology file of a strand of sequence <tt>GCGTTG</tt> would be:

<pre>
6 1
1 G -1 1
1 C 0 2
1 G 1 3
1 T 2 4
1 T 3 5
1 G 4 -1
</pre>

Specifying the topology in this way can simplify the process of simulating, for example, circular DNA.

===Generation of initial configurations===
In order to generate initial configuration and topology files, we provide the <tt>${oxDNA}/UTILS/generate-sa.py</tt> script. The usage of the script is

<pre>generate-sa.py <box side> <file with sequence></pre>

where <tt><box side></tt> specifies the length of the box side in simulation units and <tt><file with sequence></tt> contains the sequence of the strands to be generated, one row per strand. If double strands are needed, each sequence must be preceded by <tt>DOUBLE</tt>. For example, a file containing

<pre>
DOUBLE AGGGCT
CCTGTA
</pre>

would generate a double strand with a sequence <tt>AGGGCT</tt> and a single strand with a sequence <tt>CCTGTA</tt>. The sequences are given in 3'-5' order.

Positions and orientations of the strands are all chosen at random in such a way that the resulting initial configuration does not contain significant excluded volume interactions between nucleotides belonging to different strands. Generated single- and double-strands have helical conformations (i.e. they are in the minimum of the intra-strand interaction energy).

The output configuration and topology are stored in <tt>generated.dat</tt> and <tt>generated.top</tt>, respectively.
Since this script will initialize nucleotides' velocities and angular velocities to 0, when performing molecular (or Brownian) dynamics simulation remember to put <tt>refresh_vel = 1</tt> in the [[Documentation#Input_file|input]] file.

==Analysis of configurations==
The configurations produced by oxDNA can be analysed with the <tt>output_bonds</tt> program in <tt>${oxDNA}/UTILS/process_data/</tt> directory. This program takes an input the input file (to recover the temperature and topology file), a configuration/trajectory file and an optional number. Since <tt>output_bonds</tt> reads analyses a single configuration, the optional number selects the configuration which it needs to analyse in the trajectory. Analysing a whole trajectory can be done by looping over a counter.

Please note that <tt>output_bonds</tt> is not compiled automatically. If you never compiled it, do so as described in the [[Download_and_Installation#Installation|installation instructions]].

<tt>output_bonds</tt> can be used as follows:
<pre>
${oxDNA}/UTILS/process_data/output_bonds <input_file> <trajectory_file> [counter]
</pre>

The program outputs some debugging information to the standard error and information regarding the interaction energies to the standard output. The contributions arising from each of the terms in the potential (see the appendix of [[Publications|Ref. 2]]) are reported for each pair of nucleotides that have non-zero total interactions.

This output can be easily parsed to analyse the configurations.

For each pair of nucleotides that do interact in the configuration, the program prints out a line containing:
* The id of the two particles (starting from 0)
* The total interaction energy
* The hydrogen bonding (base pairing) energy
* The stacking energy
* The cross stacking energy
* The excluded volume energy
* The FENE interaction energy
* A letter indicating a status code. This will be <tt>N</tt> for pairs that interact through bonded interactions (i.e. they are neighbors along a strand) and it will be <tt>H</tt> when a base pair is present. Our definition of base pair is when two nucleotides have a hydrogen bonding energy less than 0.1 in simulation units (see [[Publications|Ref. 2]]).

===Geometry of the Model===
In the configuration/trajectory files only the positions and orientations of the nucleotides are stored. If one wants to recover the positions of the individual interaction sites in the model, some maths need to be done.

The position of the base, stacking and backbone sites can be recovered as follows:

base site: (center) + 0.40 * (axis vector)

stacking site: (center) + 0.34 * (axis vector)

backbone site: (center) - 0.40 * (axis_vector)

The picture in the [[Model_introduction|introduction]] might help understanding where the sites are.

==External Forces==
The code implements several types of external forces that can be imposed on the system that can be used either to simulate tension exerted on DNA or simply to accelerate the formation of secondary or tertiary structure. External forces can be tricky to treat, especially in a dynamics simulation, since they are an external source of work. Care should be taken in adjusting the time step, thermostat parameters and such.

To enable external forces, one needs to specify <tt>external_forces = 1</tt> in the input file and also supply an external force file to read from with the key <tt>external_forces_file = <file></tt>.

The syntax of the external forces file is quite simple. Examples of such files can be found in the [[Hairpin_formation|hairpin formation]] and [[Pseudoknot|Pseudoknot formation]] examples. Each force is specified within a block contained in curly brackets. Empty lines and lines beginning with an hash symbol (<tt>#</tt>) are ignored. Different forces require different keys to be present. If the file has the wrong syntax, oxDNA should spit out a sensible error message while parsing the file.

The different types of forces implemented at the moment are:
* harmonic trap
* string
* repulsion plane
* mutual trap

All forces act on the centre of the particle.

Forces of different kinds can be combined in the same simulation. There is a maximum number of 10 external forces per particle for memory reasons. This can be manually overridden recompiling the code with a different value of the macro <tt>MAX_EXT_FORCES</tt> (currently 10) in <tt>defs.h</tt>.

===String===
A string is implemented as a force that does not depend on the particle position. Its value can be constant or can change linearly with time. It is useful as it does not fluctuate with time.

A force of this kind is specified with <tt>type = string</tt>. The relevant keys are:
* '''particle''' (int) the particle on which to exert the force
* '''F0''' (float) the value of the force at time = 0 in simulation units (please note that the value of the time may or may not be reset when starting a simulation, depending on the input file)
* '''rate''' (float) growing rate of the force (simulation units/time steps). Typical values are very small (< 10^(-5))
* '''dir''' (3 floats separated by commas) direction of the force (automatically normalised by the code)

The following bit of code will create an external force on the first nucleotide in the system starting at 1 simulation units (48.15 pN) and growing linearly with time at the rate of 48.15pN every million time steps. The force will pull the nucleotide along the <tt>z</tt> direction.

<pre>
{
type = string
particle = 0
F0 = 1.
rate = 1e-6
dir = 0., 0., 1.
}
</pre>

===Harmonic trap===
This type of force implements an harmonic trap, of arbitrary stiffness, that can move linearly with time. It can be useful to fix the position of the nucleotides to simulate attachment to something or to implement (quasi) constant extension simulations.

A force of this kind is specified with <tt>type = trap</tt>. The relevant keys are:
* '''particle''' (int) the particle on which to exert the force
* '''pos0''' (3 floats separated by commas) rest position of the trap
* '''stiff''' (float) stiffness of the trap (the force is stiff * dx)
* '''rate''' (float) speed of the trap (length simulation units/time steps)
* '''dir''' (3 floats separated by commas) direction of movement of the trap

Here is an example input for a harmonic trap acting on the third nucleotide constraining it to stay close to the origin. In this example the trap does not move (<tt>rate=0</tt>), but one could have it move at a constant speed along the direction specified by <tt>dir</tt>, in this case the <tt>x</tt> direction.

<pre>
{
type = trap
particle = 2
pos0 = 0., 0., 0.
stiff = 1.0
rate = 0.
dir = 1.,0.,0.
}
</pre>

Please note that the trap does not comply with periodic boundary conditions. This is most likely what you want.

===Repulsion plane===
This kind of external force implements a repulsion plane that constrains a particle (or the whole system) to stay on one side of it. It is implemented as a harmonic repulsion, but the stiffness can be made arbitrarily high to mimic a hard repulsion.

A force of this kind is specified with <tt>type = repulsion_plane</tt>. The relevant keys are:
* '''particle''' (int) the particle on which to exert the force. If set to the special value -1, the force will be exerted on all particles.
* '''stiff''' (float) stiffness of the trap (the force is stiff * D, where D is distance from the plane. The force is exerted only if the nucleotide is below the plane)
* '''dir''' (3 floats separated by commas) a direction normal to the plane
* '''position''' (1 float number) specifies the position of the plane

If direction is <tt> direction = u,v,w </tt> , then the plane contains all the points (x,y,z) that satisfy the equation: u*x + v*y + w*z + position = 0.
Only nucleotides with coordinates (x,y,z) that satisfy u*x + v*y + w*z + position < 0 will feel the force.
The force exerted on a nucleotide is equal to stiff * D, where D is the distance of the nucleotide from the plane, where <math> D = | ux + vy + wz + \mbox{position}| / \sqrt{v^2 + u^2 + z^2 }.</math>
For nucleotides for which u*x + v*y + w*z + position >= 0, no force will be exerted.

Here is an example. This plane acts on the whole system and will not exert any force on nucleotides with a positive <tt>x</tt> coordinate. A force proportional to 96.3pN * (<tt>x</tt> coordinate) will be exerted on all particles .

<pre>
{
type = repulsion_plane
#whole system
particle = -1
stiff = 1. #96.3 pN in simulation units
dir = 1, 0, 0
position = 0
}
</pre>

If in the above example you would specify position = 3, then the force would be exerted on all nucleotides with coordinate x > -3.

===Mutual trap===
This force is useful to form initial configurations. It is a harmonic force that at every moment pulls a particle towards a reference particle. It is possible to specify the separation at which the force will be 0.

A force of this kind is specified with <tt>type = mutual_trap</tt>. The relevant keys are:
* '''particle''' (int) the particle on which to exert the force.
* '''ref_particle''' (int) particle to pull towards. Please note that this particle will not feel any force (the name mutual trap is thus misleading).
* '''stiff''' (float) stiffness of the trap
* '''r0''' (float) equilibrium distance of the trap.

Here is an example, extracted from the [[Pseudoknot|pseudoknot formation example]]. This will pull particle 14 towards particle 39, favouring an equilibrium distance of 1.4 (which corresponds roughly to the minimum of the hydrogen bonding potential, not a coincidence). The same force with opposite sign is exerted on particle 39 through a separate force. It is not necessary to have both particles feel the force, but it is usually works much better.

<pre>
{
type = mutual_trap
particle = 14
ref_particle = 39
stiff = 1.
r0 = 1.2
}

{
type = mutual_trap
particle = 39
ref_particle = 14
stiff = 1.
r0 = 1.2
}
</pre>

==Visualisation of structures==
oxDNA produces a trajectory file where all the relevant information is
stored. A converter is provided (<tt>traj2vis.py</tt>) in the
<tt>UTILS</tt> directory that is able to produce files in the <tt>xyz</tt>
and <tt>pdb</tt> formats. The same program can be used on a configuration
file and it will produce a snapshot.

Since the model is coearse-grained, we have to "trick" the visualisers into
thinking that the interaction sites in the model are actually atoms.
Advanced nucleic acids representations such as ribbons will not work on the
outputs.

All the images in the [[Screenshots]] page were produced with the pdb representation using UCSF chimera (see later on).

===xyz format===

just run

<pre>$oxDNA/UTILS/traj2vis.py xyz <trajectory> <topology> </pre>

(where <tt>$oxDNA</tt> is the oxDNA source directory) to get the xyz representation in a file called the same as the trajectory
file with <tt>.xyz</tt> appended. Please note that boundary conditions are
implemented strand-wise, so strands that are bound might appear at two
different sizes of the box. Also, the center of mass of the system (where
each strand is weighted the same regardless of the length) is set to 0 at
each frame. Carbons represent the backbone sites and oxygens the base sites.

The resulting file can be read with a variety of programs. Here we will
explain how to visualise it sensibly in [http://www.ks.uiuc.edu/Research/vmd/ VMD].

* Run VMD and load the xyz file.
* In the graphics menu, go to Representations.
* In the Selected Atoms line, input <tt>name C</tt>. Also select Drawing method CPK, sphere scale 0.8 and Bond Radius 0.
* In the Selected Atoms line, input <tt>name O</tt>. Also select Drawing method CPK, sphere scale 0.6 and Bond Radius 0.

This should produce a ball representation of our model DNA. Bonds
automatically produced by VMD are NOT meaningful in our context.

===pdb format===
Run

<pre>$oxDNA/UTILS/traj2vis.py xyz <trajectory> <topology> </pre>

to produce a trajectory/configuration in the pdb format. A further file
called <tt>chimera.com</tt> will be produced (more on this later). All
comments above about periodic boundaries and centre of mass apply here as
well.

The pdb file can be visualised in VMD just like the xyz format, but a nicer
output can be produced with [http://www.cgl.ucsf.edu/chimera/ UCSF Chimera] (although only for snapshots at
the moment) as follows:

Run chimera and load the pdb file. An ugly output will be displayed.

Bring up the command line under the <tt>Tools → General Controls</tt> menu.
Input <tt>read chimera.com</tt> in the command line and press enter. You
should get a nicer visualisation with different bases in different colors,
all the covalent bonds in the right place, etc.

On large configurations, the production of ellipsoids will be extremely
slow. You can remove it by removing the line

<code>aniso scale 0.75 smoothing 4</code>

from the commands file. Loading the resulting file should be much faster.

UCSF chimera can in turn export the scene in a variety of formats.

Publications

2012-09-19T17:50:36Z

Romano:

Publications

2012-09-19T17:50:28Z

Romano:

Publications

2012-09-19T17:50:06Z

Romano:

2012-09-12T17:26:03Z

Romano:

Download and Installation

2012-08-14T21:12:26Z

Romano: /* Download */

In this section, we outline the procedure for compiling oxDNA. Before starting, we recall that the only supported features of oxDNA are

*Molecular and Brownian dynamics
*Regular Monte Carlo
*External forces
*A stand-alone single- and double-strand generator (<tt>UTILS/generate-sa.py</tt>)
*An output-converter from oxDNA configuration files to .pdb and VMD-supported .xyz files (<tt>UTILS/traj2vis.py</tt>)

[[Features|This]] page contains a more detailed list.

==Requirements==
===Compiler===
The recommended compiler is gcc 4.6.x. oxDNA compilation has been thoroughly tested with gcc >= 4.1.x and icpc >= 10. Note that compiling with gcc 4.6.x rather than with gcc 4.1.x results in a significant increase in performances. Since oxDNA is writtern in standard c++, it '''should''' be also compatible with other compilers.

===Operating system===
oxDNA has been tested on Linux (kernel >= 2.6.x) and Mac OS X. Since it is written in ANSI c++, it '''should''' also work on other OSes, provided that the makefile is changed accordingly.

===Dependencies===
oxDNA does not depend on any external library apart from the standard c++ library and therefore is completely self-contained.

==Download==
The source package can be downloaded [http://pacci.phys.uniroma1.it/sites/default/files/oxdna/index.php here]. There are currently no available binary packages.

==Installation==
To install the program, untar <tt>oxDNA.tar</tt> and enter the oxDNA directory. Compile the code with

<pre>make</pre>

See [[Documentation]] for <tt>make</tt> options. If you want to compile oxDNA with the Intel C++ compiler (icpc) use

<pre>
make intel=1
</pre>

The compilation process will generate an <tt>oxDNA</tt> executable in the <tt>Release</tt> directory. The usage of oxDNA is

<pre>
oxDNA <input>
</pre>

The complete list of supported input options can be found [[Documentation#Input_file|here]]. If you want some hands-on examples, there are some in the [[Examples|EXAMPLES]] directory.

A useful analysis tool that prints out all the interactions for a configuration is in the <tt>UTILS/process_data/</tt> directory. To compile it, one needs to go into that directory and type <tt>make</tt>. The program will be called <tt>output_bonds</tt> and its usage is described in the [[Documentation#Analysis_of_configurations|Documentation]].

Download and Installation

2012-08-14T21:11:59Z

Romano: /* Download */

In this section, we outline the procedure for compiling oxDNA. Before starting, we recall that the only supported features of oxDNA are

*Molecular and Brownian dynamics
*Regular Monte Carlo
*External forces
*A stand-alone single- and double-strand generator (<tt>UTILS/generate-sa.py</tt>)
*An output-converter from oxDNA configuration files to .pdb and VMD-supported .xyz files (<tt>UTILS/traj2vis.py</tt>)

[[Features|This]] page contains a more detailed list.

==Requirements==
===Compiler===
The recommended compiler is gcc 4.6.x. oxDNA compilation has been thoroughly tested with gcc >= 4.1.x and icpc >= 10. Note that compiling with gcc 4.6.x rather than with gcc 4.1.x results in a significant increase in performances. Since oxDNA is writtern in standard c++, it '''should''' be also compatible with other compilers.

===Operating system===
oxDNA has been tested on Linux (kernel >= 2.6.x) and Mac OS X. Since it is written in ANSI c++, it '''should''' also work on other OSes, provided that the makefile is changed accordingly.

===Dependencies===
oxDNA does not depend on any external library apart from the standard c++ library and therefore is completely self-contained.

==Download==
The source package can be downloaded [http://pacci.phys.uniroma1.it/sites/default/files/oxdna/ here]. There are currently no available binary packages.

==Installation==
To install the program, untar <tt>oxDNA.tar</tt> and enter the oxDNA directory. Compile the code with

<pre>make</pre>

See [[Documentation]] for <tt>make</tt> options. If you want to compile oxDNA with the Intel C++ compiler (icpc) use

<pre>
make intel=1
</pre>

The compilation process will generate an <tt>oxDNA</tt> executable in the <tt>Release</tt> directory. The usage of oxDNA is

<pre>
oxDNA <input>
</pre>

The complete list of supported input options can be found [[Documentation#Input_file|here]]. If you want some hands-on examples, there are some in the [[Examples|EXAMPLES]] directory.

A useful analysis tool that prints out all the interactions for a configuration is in the <tt>UTILS/process_data/</tt> directory. To compile it, one needs to go into that directory and type <tt>make</tt>. The program will be called <tt>output_bonds</tt> and its usage is described in the [[Documentation#Analysis_of_configurations|Documentation]].

Download and Installation

2012-08-14T20:58:50Z

Romano: /* Download */

In this section, we outline the procedure for compiling oxDNA. Before starting, we recall that the only supported features of oxDNA are

*Molecular and Brownian dynamics
*Regular Monte Carlo
*External forces
*A stand-alone single- and double-strand generator (<tt>UTILS/generate-sa.py</tt>)
*An output-converter from oxDNA configuration files to .pdb and VMD-supported .xyz files (<tt>UTILS/traj2vis.py</tt>)

[[Features|This]] page contains a more detailed list.

==Requirements==
===Compiler===
The recommended compiler is gcc 4.6.x. oxDNA compilation has been thoroughly tested with gcc >= 4.1.x and icpc >= 10. Note that compiling with gcc 4.6.x rather than with gcc 4.1.x results in a significant increase in performances. Since oxDNA is writtern in standard c++, it '''should''' be also compatible with other compilers.

===Operating system===
oxDNA has been tested on Linux (kernel >= 2.6.x) and Mac OS X. Since it is written in ANSI c++, it '''should''' also work on other OSes, provided that the makefile is changed accordingly.

===Dependencies===
oxDNA does not depend on any external library apart from the standard c++ library and therefore is completely self-contained.

==Download==
The source package can be downloaded [http://pacci.phys.uniroma1.it/sites/default/files/oxDNA_1.0.2.tar here]. There are currently no available binary packages.

==Installation==
To install the program, untar <tt>oxDNA.tar</tt> and enter the oxDNA directory. Compile the code with

<pre>make</pre>

See [[Documentation]] for <tt>make</tt> options. If you want to compile oxDNA with the Intel C++ compiler (icpc) use

<pre>
make intel=1
</pre>

The compilation process will generate an <tt>oxDNA</tt> executable in the <tt>Release</tt> directory. The usage of oxDNA is

<pre>
oxDNA <input>
</pre>

The complete list of supported input options can be found [[Documentation#Input_file|here]]. If you want some hands-on examples, there are some in the [[Examples|EXAMPLES]] directory.

A useful analysis tool that prints out all the interactions for a configuration is in the <tt>UTILS/process_data/</tt> directory. To compile it, one needs to go into that directory and type <tt>make</tt>. The program will be called <tt>output_bonds</tt> and its usage is described in the [[Documentation#Analysis_of_configurations|Documentation]].

Download and Installation

2012-08-14T20:53:17Z

Romano: /* Download */

In this section, we outline the procedure for compiling oxDNA. Before starting, we recall that the only supported features of oxDNA are

*Molecular and Brownian dynamics
*Regular Monte Carlo
*External forces
*A stand-alone single- and double-strand generator (<tt>UTILS/generate-sa.py</tt>)
*An output-converter from oxDNA configuration files to .pdb and VMD-supported .xyz files (<tt>UTILS/traj2vis.py</tt>)

[[Features|This]] page contains a more detailed list.

==Requirements==
===Compiler===
The recommended compiler is gcc 4.6.x. oxDNA compilation has been thoroughly tested with gcc >= 4.1.x and icpc >= 10. Note that compiling with gcc 4.6.x rather than with gcc 4.1.x results in a significant increase in performances. Since oxDNA is writtern in standard c++, it '''should''' be also compatible with other compilers.

===Operating system===
oxDNA has been tested on Linux (kernel >= 2.6.x) and Mac OS X. Since it is written in ANSI c++, it '''should''' also work on other OSes, provided that the makefile is changed accordingly.

===Dependencies===
oxDNA does not depend on any external library apart from the standard c++ library and therefore is completely self-contained.

==Download==
The source package can be downloaded [http://ubuntuone.com/3feso6Dl5mh2q7tmzQkakn here]. There are currently no available binary packages.

==Installation==
To install the program, untar <tt>oxDNA.tar</tt> and enter the oxDNA directory. Compile the code with

<pre>make</pre>

See [[Documentation]] for <tt>make</tt> options. If you want to compile oxDNA with the Intel C++ compiler (icpc) use

<pre>
make intel=1
</pre>

The compilation process will generate an <tt>oxDNA</tt> executable in the <tt>Release</tt> directory. The usage of oxDNA is

<pre>
oxDNA <input>
</pre>

The complete list of supported input options can be found [[Documentation#Input_file|here]]. If you want some hands-on examples, there are some in the [[Examples|EXAMPLES]] directory.

A useful analysis tool that prints out all the interactions for a configuration is in the <tt>UTILS/process_data/</tt> directory. To compile it, one needs to go into that directory and type <tt>make</tt>. The program will be called <tt>output_bonds</tt> and its usage is described in the [[Documentation#Analysis_of_configurations|Documentation]].

MediaWiki:Sidebar

2012-07-18T14:50:27Z

Publications

2012-07-17T22:22:16Z

Romano:

Publications

2012-07-05T08:47:56Z

Romano:

2012-05-14T11:32:14Z

Romano: uploaded a new version of "Image:Cadnano 1.png"

Cadnano

2012-05-14T11:27:46Z

Romano:

[[Category:Examples]]
Cadnano is a tool for designing DNA origami structures. oxDNA includes an interface that allows origami designs generated in Cadnano to be used as starting configurations for simulation. Cadnano can also be used in this way to make non-origami structures such as DNA tiles for use in the model. It can be downloaded at http://cadnano.org/.

== Example: DX tile ==

http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/tilechimera.png

The use of Cadnano for the purpose of creating starting configurations will be illustrated using a tile similar to the DX tile. In this case Cadnano 2 will be used to design the tile, although the original Cadnano operates in a similar way and is fully compatible with the interface to oxDNA. Note that, while using cadnano, any unwanted actions can be undone with ctrl+z (this feature is new in Cadnano 2).

First click the blue "add new square lattice" button on the toolbar - a new square lattice will be created in the lattice view. The circles represent a cross-sectional view of potential DNA double helices on the square lattice. Create two empty virtual double helices in the path view by clicking on any two adjacent circles, one on top of the other. Next, using the pencil tool from the toolbar on the right, fill in all four rows in the path view by dragging from one end of each row to the other. Each double helix has two rows, and each row represents one of the strands of a double helix.

[[Image:cadnano_1a.png]]

The next step is to add the crossovers between the double helices. Using origami terminology, the thin blue lines represent the scaffold strands, while the thicker lines of different colour represent the staple strands. Make a crossover between the staple strands near the middle of the design, by first clicking on one of the staple strands near its middle and then clicking one of the numbers near the middle next to that staple strand. Also click the number just to the left or right of the crossover you just made, to make a second crossover. Do the same for the the scaffold strands - the crossovers can go either to the left or the right of the staple crossovers, not at the closest place to the staple crossovers, but the next closest place.

[[Image:cadnano_2.png]]

The tile is almost complete; the final step is to correct the lengths of the strands. Switch to the select tool and drag the ends of the strands to change their lengths. The two strands that are complementary to a double crossover should extend 8 bases past that crossover. The other two strands should extend 5 bases past those two strands. The yellow bar can help with tasks like this; drag it to any column to see the index of that column. If extra space is required, the virtual helices can be extended in either direction by clicking on the arrows at the top right of the topmost virtual helix in the path view.

[[Image:cadnano_3.png]]

The tile design is now finished and ready to be used as a starting configuration for simulation after some processing. The design can be found at ${oxDNA}/EXAMPLES/CADNANO_INTERFACE/TILE/tile.json.

== Using Cadnano Designs as Starting Configurations for oxDNA ==

The script candnano_interface.py is used to generate an oxDNA configuration and topology file from a cadnano design. In addition it creates some files containing information about the origami that can be useful later for analysing its trajectory. Its usage is

<pre>python cadnano_interface.py <cadnano_file> <design_type> [box_size]</pre>

The design type must be either sq or he, corresponding to either a square or honeycomb lattice - typically a 2D origami is on a square lattice, while a 3D origami is on a honeycomb lattice. The box size option allows the user to specify a simulation box size different to the default value of two times (in linear dimension) the largest dimension of the cadnano design.

When the configuration and topology files are first created, they cannot be used in an ordinary oxDNA simulation until they have been relaxed. This is achieved using an oxDNA MD simulation with a very low temperature and a very strongly coupled thermostat. An example input file for this simulation is found at ${oxDNA}/EXAMPLES/CADNANO_INTERFACE/input_relax. The process is very fast as the simulation need only run for around 100 steps.

For the tile discussed above, the configuration files before and after relaxation, as well as the topology file, can be found in ${oxDNA}/EXAMPLES/CADNANO_INTERFACE/TILE/.

Warning: for very large Cadnano designs, or for designs of small origamis but with very long unused sections of virtual double helices, the script requires a very large amount of memory which may cause problems!

Cadnano

2012-05-14T11:27:06Z

DsDNA persistence length

2012-05-14T10:58:51Z

Romano:

DsDNA persistence length

2012-05-14T10:58:35Z

Romano: /* Persistence length of a double-stranded DNA */

Documentation

2012-04-19T18:09:22Z

Romano: /* Analysis of configurations */

==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==

<pre>oxDNA input_file</pre>

The input file contains all the relevant information for the program to run, such as what initial configuration to use, the topology of the system, how often to print the energies to a file, etc. Please make sure you read the [[Thermostat|thermostat]] page if you use molecular dynamics.

==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; 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.

==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.

==Configuration and topology files==
The current state of a system, as by oxDNA, is described by two files: a configuration file and a topology file. The configuration file contains all the general informations (timestep, energy and box size) and orientations and positions of each nucleotide. The topology file, on the other hand, keeps track of the backbone-backbone bonds between nucleotides in the same strand. Working configuration and topology files can be found in the <tt>[[Examples|EXAMPLES]]</tt> directory.

===Configuration file===
The first three rows of a configuration file contain the timestep <tt>T</tt> at which the configuration has been printed, the length of the box sides <tt>Lx</tt>, <tt>Ly</tt> and <tt>Lz</tt> and the total, potential and kinetic energies, <tt>Etot</tt>, <tt>U</tt> and <tt>K</tt>, respectively:

<pre>
t = T
b = Lz Ly Lz
E = Etot U K
</pre>

after this header, each row contains position of the centre of mass, orientation, velocity and angular velocity of a single nucleotide in the following order:

<math>\overbrace{r_x r_y r_z}^{\rm Position} \overbrace{b_x b_y b_z}^{\rm Backbone-base versor} \overbrace{n_x n_y n_z}^{\rm Normal versor} \overbrace{v_x v_y v_z}^{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular velocity}</math>

===Topology file===
The topology file stores the intra-strand, fixed bonding topology (i.e. which nucleotides share backbone links). The first row contains the total number of nucleotides <tt>N</tt> and the number of strands <tt>Ns</tt>:

<code>
N Ns
</code>

After this header, the <tt>i</tt>-th row specifies strand, base and 3' and 5' neighbors of the <tt>i</tt>-th nucleotide in this way:

<code>
S B 3' 5'
</code>

where S is the number of the strand (starting from 1) which the nucleotide belongs to, B is the base and 3' and 5' specify the index of the nucleotides with which the <tt>i</tt>-th nucleotide is bonded in the 3' and 5' direction, respectively. A <tt>-1</tt> signals that the nucleotide terminates the strand in either 3' or 5' direction. The topology file of a strand of sequence <tt>GCGTTG</tt> would be:

<pre>
6 1
1 G -1 1
1 C 0 2
1 G 1 3
1 T 2 4
1 T 3 5
1 G 4 -1
</pre>

Specifying the topology in this way can simplify the process of simulating, for example, circular DNA.

===Generation of initial configurations===
In order to generate initial configuration and topology files, we provide the <tt>${oxDNA}/UTILS/generate-sa.py</tt> script. The usage of the script is

<pre>generate-sa.py <box side> <file with sequence></pre>

where <tt><box side></tt> specifies the length of the box side in simulation units and <tt><file with sequence></tt> contains the sequence of the strands to be generated, one row per strand. If double strands are needed, each sequence must be preceded by <tt>DOUBLE</tt>. For example, a file containing

<pre>
DOUBLE AGGGCT
CCTGTA
</pre>

would generate a double strand with a sequence <tt>AGGGCT</tt> and a single strand with a sequence <tt>CCTGTA</tt>.

Positions and orientations of the strands are all chosen at random in such a way that the resulting initial configuration does not contain significant excluded volume interactions between nucleotides belonging to different strands. Generated single- and double-strands have helical conformations (i.e. they are in the minimum of the intra-strand interaction energy).

The output configuration and topology are stored in <tt>generated.dat</tt> and <tt>generated.top</tt>, respectively.
Since this script will initialize nucleotides' velocities and angular velocities to 0, when performing molecular (or Brownian) dynamics simulation remember to put <tt>refresh_vel = 1</tt> in the [[Documentation#Input_file|input]] file.

==Analysis of configurations==
The configurations produced by oxDNA can be analysed with the <tt>output_bonds</tt> program in <tt>${oxDNA}/UTILS/process_data/</tt> directory. This program takes an input the input file (to recover the temperature and topology file), a configuration/trajectory file and an optional number. Since <tt>output_bonds</tt> reads analyses a single configuration, the optional number selects the configuration which it needs to analyse in the trajectory. Analysing a whole trajectory can be done by looping over a counter.

Please note that <tt>output_bonds</tt> is not compiled automatically. If you never compiled it, do so as described in the [[Download_and_Installation#Installation|installation instructions]].

<tt>output_bonds</tt> can be used as follows:
<pre>
${oxDNA}/UTILS/process_data/output_bonds <input_file> <trajectory_file> [counter]
</pre>

The program outputs some debugging information to the standard error and information regarding the interaction energies to the standard output. The contributions arising from each of the terms in the potential (see the appendix of [[Publications|Ref. 2]]) are reported for each pair of nucleotides that have non-zero total interactions.

This output can be easily parsed to analyse the configurations.

For each pair of nucleotides that do interact in the configuration, the program prints out a line containing:
* The id of the two particles (starting from 0)
* The total interaction energy
* The hydrogen bonding (base pairing) energy
* The stacking energy
* The cross stacking energy
* The excluded volume energy
* The FENE interaction energy
* A letter indicating a status code. This will be <tt>N</tt> for pairs that interact through bonded interactions (i.e. they are neighbors along a strand) and it will be <tt>H</tt> when a base pair is present. Our definition of base pair is when two nucleotides have a hydrogen bonding energy less than 0.1 in simulation units (see [[Publications|Ref. 2]]).

===Geometry of the Model===
In the configuration/trajectory files only the positions and orientations of the nucleotides are stored. If one wants to recover the positions of the individual interaction sites in the model, some maths need to be done.

The position of the base, stacking and backbone sites can be recovered as follows:

base site: (center) + 0.40 * (axis vector)

stacking site: (center) + 0.34 * (axis vector)

backbone site: (center) - 0.40 * (axis_vector)

The picture in the [[Model_introduction|introduction]] might help understanding where the sites are.

==External Forces==
The code implements several types of external forces that can be imposed on the system that can be used either to simulate tension exerted on DNA or simply to accelerate the formation of secondary or tertiary structure. External forces can be tricky to treat, especially in a dynamics simulation, since they are an external source of work. Care should be taken in adjusting the time step, thermostat parameters and such.

To enable external forces, one needs to specify <tt>external_forces = 1</tt> in the input file and also supply an external force file to read from with the key <tt>external_forces_file = <file></tt>.

The syntax of the external forces file is quite simple. Examples of such files can be found in the [[Hairpin_formation|hairpin formation]] and [[Pseudoknot|Pseudoknot formation]] examples. Each force is specified within a block contained in curly brackets. Empty lines and lines beginning with an hash symbol (<tt>#</tt>) are ignored. Different forces require different keys to be present. If the file has the wrong syntax, oxDNA should spit out a sensible error message while parsing the file.

The different types of forces implemented at the moment are:
* harmonic trap
* string
* repulsion plane
* mutual trap

All forces act on the centre of the particle.

Forces of different kinds can be combined in the same simulation. There is a maximum number of 10 external forces per particle for memory reasons. This can be manually overridden recompiling the code with a different value of the macro <tt>MAX_EXT_FORCES</tt> (currently 10) in <tt>defs.h</tt>.

===String===
A string is implemented as a force that does not depend on the particle position. Its value can be constant or can change linearly with time. It is useful as it does not fluctuate with time.

A force of this kind is specified with <tt>type = string</tt>. The relevant keys are:
* '''particle''' (int) the particle on which to exert the force
* '''F0''' (float) the value of the force at time = 0 in simulation units (please note that the value of the time may or may not be reset when starting a simulation, depending on the input file)
* '''rate''' (float) growing rate of the force (simulation units/time steps). Typical values are very small (< 10^(-5))
* '''dir''' (3 floats separated by commas) direction of the force (automatically normalised by the code)

The following bit of code will create an external force on the first nucleotide in the system starting at 1 simulation units (48.15 pN) and growing linearly with time at the rate of 48.15pN every million time steps. The force will pull the nucleotide along the <tt>z</tt> direction.

<pre>
{
type = string
particle = 0
F0 = 1.
rate = 1e-6
dir = 0., 0., 1.
}
</pre>

===Harmonic trap===
This type of force implements an harmonic trap, of arbitrary stiffness, that can move linearly with time. It can be useful to fix the position of the nucleotides to simulate attachment to something or to implement (quasi) constant extension simulations.

A force of this kind is specified with <tt>type = trap</tt>. The relevant keys are:
* '''particle''' (int) the particle on which to exert the force
* '''pos0''' (3 floats separated by commas) rest position of the trap
* '''stiff''' (float) stiffness of the trap (the force is stiff * dx)
* '''rate''' (float) speed of the trap (length simulation units/time steps)
* '''dir''' (3 floats separated by commas) direction of movement of the trap

Here is an example input for a harmonic trap acting on the third nucleotide constraining it to stay close to the origin. In this example the trap does not move (<tt>rate=0</tt>), but one could have it move at a constant speed along the direction specified by <tt>dir</tt>, in this case the <tt>x</tt> direction.

<pre>
{
type = trap
particle = 2
pos0 = 0., 0., 0.
stiff = 1.0
rate = 0.
dir = 1.,0.,0.
}
</pre>

Please note that the trap does not comply with periodic boundary conditions. This is most likely what you want.

===Repulsion plane===
This kind of external force implements a repulsion plane that constrains a particle (or the whole system) to stay on one side of it. It is implemented as a harmonic repulsion, but the stiffness can be made arbitrarily high to mimic a hard repulsion.

A force of this kind is specified with <tt>type = repulsion_plane</tt>. The relevant keys are:
* '''particle''' (int) the particle on which to exert the force. If set to the special value -1, the force will be exerted on all particles.
* '''stiff''' (float) stiffness of the trap (the force is stiff * D, where D is distance from the plane. The force is exerted only if the nucleotide is below the plane)
* '''dir''' (3 floats separated by commas) a direction normal to the plane
* '''position''' (1 float number) specifies the position of the plane

If direction is <tt> direction = u,v,w </tt> , then the plane contains all the points (x,y,z) that satisfy the equation: u*x + v*y + w*z + position = 0.
Only nucleotides with coordinates (x,y,z) that satisfy u*x + v*y + w*z + position < 0 will feel the force.
The force exerted on a nucleotide is equal to stiff * D, where D is the distance of the nucleotide from the plane, where <tt> D = | u*x + v*y + w*z + position | / \sqrt(v^2 + u^2 + z^2 ).</tt>
For nucleotides for which u*x + v*y + w*z + position >= 0, no force will be exerted.

Here is an example. This plane acts on the whole system and will not exert any force on nucleotides with a positive <tt>x</tt> coordinate. A force proportional to 96.3pN * (<tt>x</tt> coordinate) will be exerted on all particles .

<pre>
{
type = repulsion_plane
#whole system
particle = -1
stiff = 1. #96.3 pN in simulation units
dir = 1, 0, 0
position = 0
}
</pre>

If in the above example you would specify position = 3, then the force would be exerted on all nucleotides with coordinate x > -3.

===Mutual trap===
This force is useful to form initial configurations. It is a harmonic force that at every moment pulls a particle towards a reference particle. It is possible to specify the separation at which the force will be 0.

A force of this kind is specified with <tt>type = mutual_trap</tt>. The relevant keys are:
* '''particle''' (int) the particle on which to exert the force.
* '''ref_particle''' (int) particle to pull towards. Please note that this particle will not feel any force (the name mutual trap is thus misleading).
* '''stiff''' (float) stiffness of the trap
* '''r0''' (float) equilibrium distance of the trap.
* '''position''' (3 floats separated by commas) one point belonging to the plane.

Here is an example, extracted from the [[Pseudoknot|pseudoknot formation example]]. This will pull particle 14 towards particle 39, favouring an equilibrium distance of 1.4 (which corresponds roughly to the minimum of the hydrogen bonding potential, not a coincidence). The same force with opposite sign is exerted on particle 39 through a separate force. It is not necessary to have both particles feel the force, but it is usually works much better.

<pre>
{
type = mutual_trap
particle = 14
ref_particle = 39
stiff = 1.
r0 = 1.2
}

{
type = mutual_trap
particle = 39
ref_particle = 14
stiff = 1.
r0 = 1.2
}
</pre>

==Visualisation of structures==
oxDNA produces a trajectory file where all the relevant information is
stored. A converter is provided (<tt>traj2vis.py</tt>) in the
<tt>UTILS</tt> directory that is able to produce files in the <tt>xyz</tt>
and <tt>pdb</tt> formats. The same program can be used on a configuration
file and it will produce a snapshot.

Since the model is coearse-grained, we have to "trick" the visualisers into
thinking that the interaction sites in the model are actually atoms.
Advanced nucleic acids representations such as ribbons will not work on the
outputs.

All the images in the [[Screenshots]] page were produced with the pdb representation using UCSF chimera (see later on).

===xyz format===

just run

<pre>$oxDNA/UTILS/traj2vis.py xyz <trajectory> <topology> </pre>

(where <tt>$oxDNA</tt> is the oxDNA source directory) to get the xyz representation in a file called the same as the trajectory
file with <tt>.xyz</tt> appended. Please note that boundary conditions are
implemented strand-wise, so strands that are bound might appear at two
different sizes of the box. Also, the center of mass of the system (where
each strand is weighted the same regardless of the length) is set to 0 at
each frame. Carbons represent the backbone sites and oxygens the base sites.

The resulting file can be read with a variety of programs. Here we will
explain how to visualise it sensibly in [http://www.ks.uiuc.edu/Research/vmd/ VMD].

* Run VMD and load the xyz file.
* In the graphics menu, go to Representations.
* In the Selected Atoms line, input <tt>name C</tt>. Also select Drawing method CPK, sphere scale 0.8 and Bond Radius 0.
* In the Selected Atoms line, input <tt>name O</tt>. Also select Drawing method CPK, sphere scale 0.6 and Bond Radius 0.

This should produce a ball representation of our model DNA. Bonds
automatically produced by VMD are NOT meaningful in our context.

===pdb format===
Run

<pre>$oxDNA/UTILS/traj2vis.py xyz <trajectory> <topology> </pre>

to produce a trajectory/configuration in the pdb format. A further file
called <tt>chimera.com</tt> will be produced (more on this later). All
comments above about periodic boundaries and centre of mass apply here as
well.

The pdb file can be visualised in VMD just like the xyz format, but a nicer
output can be produced with [http://www.cgl.ucsf.edu/chimera/ UCSF Chimera] (although only for snapshots at
the moment) as follows:

Run chimera and load the pdb file. An ugly output will be displayed.

Bring up the command line under the <tt>Tools → General Controls</tt> menu.
Input <tt>read chimera.com</tt> in the command line and press enter. You
should get a nicer visualisation with different bases in different colors,
all the covalent bonds in the right place, etc.

On large configurations, the production of ellipsoids will be extremely
slow. You can remove it by removing the line

<code>aniso scale 0.75 smoothing 4</code>

from the commands file. Loading the resulting file should be much faster.

UCSF chimera can in turn export the scene in a variety of formats.

Download and Installation

2012-04-19T18:07:32Z

Romano: /* Installation */

In this section, we outline the procedure for compiling oxDNA. Before starting, we recall that the only supported features of oxDNA are

*Molecular and Brownian dynamics
*Regular Monte Carlo
*External forces
*A stand-alone single- and double-strand generator (<tt>UTILS/generate-sa.py</tt>)
*An output-converter from oxDNA configuration files to .pdb and VMD-supported .xyz files (<tt>UTILS/traj2vis.py</tt>)

[[Features|This]] page contains a more detailed list.

==Requirements==
===Compiler===
The recommended compiler is gcc 4.6.x. oxDNA compilation has been thoroughly tested with gcc >= 4.1.x and icpc >= 10. Note that compiling with gcc 4.6.x rather than with gcc 4.1.x results in a significant increase in performances. Since oxDNA is writtern in standard c++, it '''should''' be also compatible with other compilers.

===Operating system===
oxDNA has been tested on Linux (kernel >= 2.6.x) and Mac OS X. Since it is written in ANSI c++, it '''should''' also work on other OSes, provided that the makefile is changed accordingly.

===Dependencies===
oxDNA does not depend on any external library apart from the standard c++ library and therefore is completely self-contained.

==Download==
The source package can be downloaded [http://kratos.phys.uniroma1.it/download_oxdna_code.php here]. There are currently no available binary packages.

==Installation==
To install the program, untar <tt>oxDNA.tar.gz</tt> and enter the oxDNA directory. Compile the code with

<pre>make</pre>

See [[Documentation]] for <tt>make</tt> options. If you want to compile oxDNA with the Intel C++ compiler (icpc) use

<pre>
make intel=1
</pre>

The compilation process will generate an <tt>oxDNA</tt> executable in the <tt>Release</tt> directory. The usage of oxDNA is

<pre>
oxDNA <input>
</pre>

The complete list of supported input options can be found [[Documentation#Input_file|here]]. If you want some hands-on examples, there are some in the [[Examples|EXAMPLES]] directory.

A useful analysis tool that prints out all the interactions for a configuration is in the <tt>UTILS/process_data/</tt> directory. To compile it, one needs to go into that directory and type <tt>make</tt>. The program will be called <tt>output_bonds</tt> and its usage is described in the [[Documentation#Analysis_of_configurations|Documentation]].