Download and Installation of do_x3dna for GROMACS

Download

do_x3dna package 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 one of the following versions of Gromacs:

  • Gromacs-4.5.x
  • Gromacs-4.6.x
  • Gromacs-5.0.x
  • Gromacs-5.1.x
  • Gromacs-2016.x
  • Gromacs-2018.x

For Gromacs 4.5.x and 4.6.x versions libraries such as libmd.a/.so, libgmx.a/.so and libgmxana.a/.so are required.

For Gromacs 5.0.x, 5.1.x, 2016.x and 2018.x version libgromacs.a/.so is required.

Steps

Follow these steps to install do_x3dna

cd do_x3dna
mkdir build
cd build
cmake ..  -DGMX_PATH=/opt/gromacs -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.

  • -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.