Download and 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 (UTILS/generate-sa.py)
• An output-converter from oxDNA configuration files to .pdb and VMD-supported .xyz files (UTILS/traj2vis.py)

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 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 oxDNA.tar and enter the oxDNA directory. Compile the code with

make

See Documentation for make options. If you want to compile oxDNA with the Intel C++ compiler (icpc) use

make intel=1

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

oxDNA <input>

The complete list of supported input options can be found here. If you want some hands-on examples, there are some in the EXAMPLES directory.

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