Features of the previous version - Revision history

Rovigattil: moved Features previous to Features of the previous version

2014-03-19T10:47:08Z

moved Features previous to Features of the previous version

← Older revision	Revision as of 10:47, 19 March 2014
(No difference)

Rovigattil: moved Features to Features previous

2014-03-19T10:39:06Z

moved Features to Features previous

← Older revision	Revision as of 10:39, 19 March 2014
(No difference)

Sulc at 17:38, 17 March 2014

2014-03-17T17:38:38Z

← Older revision		Revision as of 17:38, 17 March 2014
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	*CUDA version of the Brownian dynamics code (which is not included in the source file, but available upon request)		*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 molecular 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.

Snodinb: /* Experimental (Unsupported) features */

2013-11-18T12:31:52Z

Experimental (Unsupported) features

← Older revision		Revision as of 12:31, 18 November 2013
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	==Experimental (Unsupported) features==		==Experimental (Unsupported) features==
	The released version of oxDNA contains ~~also~~ code for		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)		*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		*Cluster-Move Monte Carlo (CMMC) 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		*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.

Snodinb: /* Supported features */

2013-11-18T12:16:37Z

Supported features

← Older revision		Revision as of 12:16, 18 November 2013
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	;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>

Sulc: /* Experimental (Unsupported) features */

2013-07-19T04:27:54Z

Experimental (Unsupported) features

← Older revision		Revision as of 04:27, 19 July 2013
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	The released version of oxDNA contains also code for		The released version of oxDNA contains also 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)		*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		*Cluster-Move Monte Carlo (CMMC) simulations

Romano: /* Supported features */

2012-05-14T14:29:10Z

Supported features

← Older revision		Revision as of 14:29, 14 May 2012
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	;Cadnano converter		;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.		: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==

Romano: /* Supported features */

2012-05-14T14:28:20Z

Supported features

← Older revision		Revision as of 14:28, 14 May 2012
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	: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==

Sulc at 14:05, 25 April 2012

2012-04-25T14:05:28Z

← Older revision		Revision as of 14:05, 25 April 2012
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	*MPI-powered parallel energy calculation		*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		*Cluster-Move Monte Carlo (CMMC) simulations
	*Forward Flux Sampling moleculary dynamics simulations		*Forward Flux Sampling moleculary dynamics simulations

Romano at 01:21, 18 April 2012

2012-04-18T01:21:24Z

← Older revision		Revision as of 01:21, 18 April 2012
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	: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].

	==Unsupported features==		==Experimental (Unsupported) features==
	The released version of oxDNA contains also code for		The released version of oxDNA contains also code for

	*MPI-powered parallel energy calculation		*MPI-powered parallel energy calculation
	*Cluster-Move Monte Carlo (CMMC) simulations		*Cluster-Move Monte Carlo (CMMC) simulations