Difference between revisions of "Features of the previous version"

From OxDNA
 
(8 intermediate revisions by 4 users not shown)
Line 4: Line 4:
 
;Molecular and Brownian dynamics: The code can run both NVE and NVT simulations. The NVT ensemble can be enforced with two different kinds of [[Documentation#Molecular_dynamics_simulations_options|thermostats]].
 
;Molecular and Brownian dynamics: The code can run both NVE and NVT simulations. The NVT ensemble can be enforced with two different kinds of [[Documentation#Molecular_dynamics_simulations_options|thermostats]].
  
;Regular Monte Carlo: regular Metropolis Monte Carlo simulations, with only nucleotide roto-translational moves, can be performed.
+
;Regular Monte Carlo: Regular Metropolis Monte Carlo simulations, with only nucleotide roto-translational moves, can be performed.
  
;External forces: in order to favor motif formation or to mimic different external environments, different kind of forces can be applied to nucleotides or points in space. The complete list of available external forces can be found in the [[Documentation|documentation]].
+
;External forces: In order to favor motif formation or to mimic different external environments, different kind of forces can be applied to nucleotides or points in space. The complete list of available external forces can be found in the [[Documentation|documentation]].
  
;Standalone single- and double-strand generator: we provide a script (<tt>[[Documentation#Generation_of_initial_configurations|UTILS/generate-sa.py]]</tt>) which can be used to generate oxDNA input configurations with the command  
+
;Standalone single- and double-strand generator: We provide a script (<tt>[[Documentation#Generation_of_initial_configurations|UTILS/generate-sa.py]]</tt>) which can be used to generate oxDNA input configurations with the command  
  
:<pre>generate-sa.py<box side> <file with sequence></pre>  
+
:<pre>generate-sa.py <box side> <file with sequence></pre>  
  
 
:<tt><box side></tt> specifies the length of the box side in simulation units, while <tt><file with sequence></tt> must contain 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>.
 
:<tt><box side></tt> specifies the length of the box side in simulation units, while <tt><file with sequence></tt> must contain 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>.
  
;Output converter: we provide a script (<tt>[[Documentation#Visualisation_of_structures|UTILS/traj2vis.py]]</tt>) which converts oxDNA configuration files to .pdb and [http://www.ks.uiuc.edu/Research/vmd/ VMD]-supported .xyz files. The usage is  
+
;Output converter: We provide a script (<tt>[[Documentation#Visualisation_of_structures|UTILS/traj2vis.py]]</tt>) which converts oxDNA configuration files to .pdb and [http://www.ks.uiuc.edu/Research/vmd/ VMD]-supported .xyz files. The usage is  
  
 
:<pre>traj2vis.py <pdb|xyz> <trajectory> <topology></pre>
 
:<pre>traj2vis.py <pdb|xyz> <trajectory> <topology></pre>
  
 
:where the output format is either pdb or xyz, <tt><trajectory></tt> is the configuration (or whole trajectory) file and <tt><topology></tt> is the topology file. The output filename is <trajectory>.pdb or <trajectory>.xyz, depending on which output format has been chosen. If <tt>pdb</tt> is selected, then a <tt>commands.com</tt> file is generated, to be used with [http://www.cgl.ucsf.edu/chimera/ UCSF Chimera].
 
:where the output format is either pdb or xyz, <tt><trajectory></tt> is the configuration (or whole trajectory) file and <tt><topology></tt> is the topology file. The output filename is <trajectory>.pdb or <trajectory>.xyz, depending on which output format has been chosen. If <tt>pdb</tt> is selected, then a <tt>commands.com</tt> file is generated, to be used with [http://www.cgl.ucsf.edu/chimera/ UCSF Chimera].
 +
 +
;Cadnano converter
 +
:There is a converter that takes [http://cadnano.org cadnano] files and converts them in initial configurations to be fed to the simulation program. See [[Cadnano]] for an example on how to use it.
  
 
==Experimental (Unsupported) features==
 
==Experimental (Unsupported) features==
The released version of oxDNA contains also code for
+
The released version of oxDNA also contains code for
  
*MPI-powered parallel energy calculation
+
*CUDA version of the Brownian dynamics code (which is not included in the source file, but available upon request)
*Cluster-Move Monte Carlo (CMMC) simulations
+
*Virtual Move Monte Carlo (VMMC) simulations
*Forward Flux Sampling moleculary dynamics simulations
+
*Forward Flux Sampling molecular dynamics simulations
 
*Umbrella Sampling simulations
 
*Umbrella Sampling simulations
*Frenkel-Ladd CMMC free energy calculation
 
 
*A huge number of utility scripts which make working with strands easier. They are contained in the <tt>UTILS</tt> directory.
 
*A huge number of utility scripts which make working with strands easier. They are contained in the <tt>UTILS</tt> directory.

Latest revision as of 10:47, 19 March 2014

Since oxDNA is still in its early stages of development, we release the code as-is with all the features enabled but we only give support to some of them. In particular, we provide examples and support to only molecular dynamics, Brownian dynamics and regular Monte Carlo simulations.

Supported features

Molecular and Brownian dynamics
The code can run both NVE and NVT simulations. The NVT ensemble can be enforced with two different kinds of thermostats.
Regular Monte Carlo
Regular Metropolis Monte Carlo simulations, with only nucleotide roto-translational moves, can be performed.
External forces
In order to favor motif formation or to mimic different external environments, different kind of forces can be applied to nucleotides or points in space. The complete list of available external forces can be found in the documentation.
Standalone single- and double-strand generator
We provide a script (UTILS/generate-sa.py) which can be used to generate oxDNA input configurations with the command
generate-sa.py <box side> <file with sequence>
<box side> specifies the length of the box side in simulation units, while <file with sequence> must contain the sequence of the strands to be generated, one row per strand. If double strands are needed, each sequence must be preceded by DOUBLE:.
Output converter
We provide a script (UTILS/traj2vis.py) which converts oxDNA configuration files to .pdb and VMD-supported .xyz files. The usage is
traj2vis.py <pdb|xyz> <trajectory> <topology>
where the output format is either pdb or xyz, <trajectory> is the configuration (or whole trajectory) file and <topology> is the topology file. The output filename is <trajectory>.pdb or <trajectory>.xyz, depending on which output format has been chosen. If pdb is selected, then a commands.com file is generated, to be used with UCSF Chimera.
Cadnano converter
There is a converter that takes cadnano files and converts them in initial configurations to be fed to the simulation program. See Cadnano for an example on how to use it.

Experimental (Unsupported) features

The released version of oxDNA also contains code for

  • CUDA version of the Brownian dynamics code (which is not included in the source file, but available upon request)
  • Virtual Move Monte Carlo (VMMC) simulations
  • Forward Flux Sampling molecular dynamics simulations
  • Umbrella Sampling simulations
  • A huge number of utility scripts which make working with strands easier. They are contained in the UTILS directory.