Download and Installation: Difference between revisions
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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. | 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]]. | |||
Revision as of 18:07, 19 April 2012
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.
Installation
To install the program, untar oxDNA.tar.gz 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.