Previous version

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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 make 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 (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.

Compilation

To install the program, untar oxDNA.tar and enter the oxDNA directory. Compile the code with

make

Compile options

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:

  • 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 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.