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.

Quick Installation

Direct use of binary executable is recommended. The binary executable of do_x3dna is available for direct download from here.

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/.

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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

  1. Download either zipball or tarball.

Installation

do_x3dna requires GROMACS-2023.

Steps

Follow these steps to install do_x3dna

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.