Download and Installation of do_x3dna for GROMACS
Warning
DSSR-X3DNA is incompatible with do_x3dna. Please use original 3DNA packacge. This could be dowloaded from by 3DNA forum.
Download
do_x3dna package can be downloaded by either of following two steps.
Use
git
:
git clone -b master --single-branch https://github.com/rjdkmr/do_x3dna
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-2023.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$HOME/bin
directory.Instead of
GMX_PATH
,CMAKE_PREFIX_PATH
can be used before running cmake as follows:
export CMAKE_PREFIX_PATH=/opt/gromacs
export CMAKE_PREFIX_PATH=/opt/gromacs:/path/to/fftw
In case of ERROR: FFTW library file libfftw3f.so or libfftw3f.a not found… use
-DFFTW_LIB=/path/to/fftw/lib/
to give a path for the directory containing either of the two files.
Installation for older GROMACS versions
do_x3dna requires one of the following older GROMACS:
Gromacs-4.5.x
Gromacs-4.6.x
Gromacs-5.0.x
Gromacs-5.1.x
Gromacs-2016.x
Gromacs-2018.x
For Gromacs 4.5.x and 4.6.x versions libraries such as libmd.a/.so
,
libgmx.a/.so
and libgmxana.a/.so
are required.
For Gromacs 5.0.x, 5.1.x, 2016.x and 2018.x version libgromacs.a/.so
is
required.
Steps
Follow these steps to install do_x3dna
cd do_x3dna
git checkout 2018 # Checkout 2018 branch for older gromacs version
mkdir build
cd build
cmake .. -DGMX_PATH=/opt/gromacs -DCMAKE_INSTALL_PREFIX=/opt/do_x3dna
make
sudo make install
Directory /opt/gromacs
should contains include
and lib
directories.
Gromacs version will be automatically detected and accordingly processed during
compilations.
-DGMX_PATH
: path to GROMACS installation directory.
-DCMAKE_INSTALL_PREFIX
: path to a directory where do_x3dna will be installed. If this option is not provided, do_x3dna will install either in/usr/local/bin
or in$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.