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Rovigattil at 10:47, 19 March 2014

2014-03-19T10:47:36Z

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	*An output-converter from oxDNA configuration files to .pdb and VMD-supported .xyz files (<tt>UTILS/traj2vis.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.		[[Features_of_the_previous_version\|This]] page contains a more detailed list.

	==Requirements==		==Requirements==

Rovigattil: /* Installation */

2014-03-18T07:08:25Z

Installation

← Older revision		Revision as of 07:08, 18 March 2014
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	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.		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~~==		==Compilation==
	To install the program, untar <tt>oxDNA.tar</tt> and enter the oxDNA directory. Compile the code with		To install the program, untar <tt>oxDNA.tar</tt> and enter the oxDNA directory. Compile the code with

	<pre>make</pre>		<pre>make</pre>

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

	~~<pre>~~		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:
	~~make~~ intel=1
	~~</pre>~~		*'''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.

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

Rovigattil: /* Download */

2014-03-18T07:07:03Z

Download

← Older revision		Revision as of 07:07, 18 March 2014
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	==Download==		==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.		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.
	~~A new version, more extensible and redesigned to provide additional flexibility, will be released soon. A pre-release of this new oxDNA is available upon request~~.

	==Installation==		==Installation==

Sulc at 00:54, 18 March 2014

2014-03-18T00:54:32Z

← Older revision		Revision as of 00:54, 18 March 2014
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			In this section, we outline the procedure for compiling the previously released (2012) version of oxDNA simulation code. This version is no longer developed, but the links for the download and installation instructions are provided below for convenience. We note that the 2012 version of oxDNA requires <tt>make</tt> software and a C++ compiler.
	In this section, we outline the procedure for compiling the previously released (2012) version of oxDNA simulation code. This version is no longer developed ~~or supported~~, but the links for the download and installation instructions are provided below for convenience. We note that the 2012 version of oxDNA requires <tt>make</tt> software and a C++ compiler.

Sulc: Created page with " In this section, we outline the procedure for compiling the previously released (2012) version of oxDNA simulation code. This version is no longer developed or supported, but th…"

2014-03-17T17:36:02Z

Created page with " In this section, we outline the procedure for compiling the previously released (2012) version of oxDNA simulation code. This version is no longer developed or supported, but th…"

New page

In this section, we outline the procedure for compiling the previously released (2012) version of oxDNA simulation code. This version is no longer developed or supported, but the links for the download and installation instructions are provided below for convenience. We note that the 2012 version of oxDNA requires <tt>make</tt> software and a C++ compiler.

Before starting, we recall that the 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.
A new version, more extensible and redesigned to provide additional flexibility, will be released soon. A pre-release of this new oxDNA is available upon request.

==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]].