Download and Installation new

In this section, we outline the procedure for compiling oxDNA.

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. Optionally, oxDNA can be compiled to run on NVIDIA GPUs by enabling CUDA support at compile time.

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 out-of-the-box on other OSes.

Dependencies

The pre-compilation stage requires cmake, while compilation is carried out with GNU Make.

The CPU-only oxDNA does not depend on any external library apart from the standard c++ library.

The GPU-enabled oxDNA requires CUDA >= 3.2.

Download

There are currently no available binary packages for oxDNA. The last stable source package can be downloaded here, while bleeding edge (possibly unstable) versions are available via a subversion repository, accessible here.

Installation

To install the program 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.