Download and Installation of do_x3dna
=====================================

.. warning:: DSSR-X3DNA is incompatible with do_x3dna. Please use original 3DNA packacge.
          This could be downloaded from by `3DNA forum <http://forum.x3dna.org/site-announcements/download-instructions/>`_.

Quick Installation
------------------

Direct use of binary executable is recommended. The binary executable of do_x3dna is available for 
direct `download from here <https://rjdkmr.github.io/do_x3dna/binary/do_x3dna.tar.gz>`_.

.. note:: This binary executable can be used with files generated by any version of GROMACS.

It can be installed as follows:
::
  
    tar -xvzf do_x3dna.tar.gz
    sudo cp -r do_x3dna/do_x3dna /usr/local/bin/.


---

Installation from source code
-----------------------------

.. warning:: Installation from source requires GROMACS to be built with additional `cmake` flag `-DGMX_INSTALL_LEGACY_API=on`.

Download
________

**do_x3dna source-code can be downloaded by either of following two steps.**

1. Use ``git``:

::

    git clone -b master --single-branch https://github.com/rjdkmr/do_x3dna


2. Download either `zipball <https://github.com/rjdkmr/do_x3dna/archive/master.zip>`_ or `tarball <https://github.com/rjdkmr/do_x3dna/archive/master.tar.gz>`_.

Installation
____________
do_x3dna requires GROMACS-2023.

Steps
+++++
Follow these steps to install do_x3dna

.. code-block:: bash

    cd do_x3dna
    mkdir build
    cd build
    cmake ..  -DGMX_PATH=/opt/gromacs -DGMX_SRC=/path/to/gromacs-2025.x -DCMAKE_INSTALL_PREFIX=/opt/do_x3dna
    make
    sudo make install


Directory ``/opt/gromacs`` should contains ``include`` and ``lib`` directories.
Gromacs version will be automatically detected and accordingly processed during
compilations.

  * ``-DGMX_PATH`` : path to GROMACS installation directory.

  * ``-DGMX_SRC`` : path to GROMACS source code directory downloaded from GROMACS download page.

  * ``-DCMAKE_INSTALL_PREFIX``: path to a directory where do_x3dna will be installed.
    If this option is not provided, do_x3dna will install either in ``/usr/local/bin``
    or in ``$HOME/bin`` directory.

  * Instead of ``GMX_PATH``, ``CMAKE_PREFIX_PATH`` can be used before running cmake as follows:

      * ``export CMAKE_PREFIX_PATH=/opt/gromacs``
      * ``export CMAKE_PREFIX_PATH=/opt/gromacs:/path/to/fftw``

  * In case of **ERROR**: **FFTW library file libfftw3f.so or libfftw3f.a not found...**
    use ``-DFFTW_LIB=/path/to/fftw/lib/`` to give a path for the directory containing either of the two files.