Installation of Gromacs-5.1.4
First and foremost, you need to get the source files (with .tar.gz extension) from homepage of Gromacs. Then open a terminal and type the following command:
<![CDATA[tar -xzvf gromacs-5.1.4.tar.gz
cd gromacs-5.1.4
mkdir build
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This extracts the files from the .tar.gz file to a folder with the same file name and creates a build directory.
<![CDATA[mkdir /home/username/gromacs_bin
cmake /home/username/gromacs-5.1.4 -DCMAKE_PREFIX_PATH=/home/username/fftw_bin/include:
/home/username/fftw_bin/lib -DFFTWF_INCLUDE_DIR=/home/username/fftw_bin/include:
/home/username/fftw_bin/lib
-DFFTWF_LIBRARY=/home/username/fftw_bin/lib/libfftw3f.so
-DCMAKE_INSTALL_PREFIX=/home/username/gromacs_bin
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And in fact, I have no idea why cmake has such a complex and long option name, which makes this command look so intimidating. If everything goes fine, please go to the directory /home/username/gromacs-5.1.4/src/gromacs/fft/ and change the follwing lines in the fft5d.h as well as fft_fftw3.ccp file from:
#include <fftw3.h>
to
#include </home/username/fftw_bin/include/fftw3.h>
We can then run the make command for the installation.
<![CDATA[make prefix=/home/username/gromacs_bin
make prefix=/home/username/gromacs_bin install
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After the installation, you have to include the directory path in the .bash_profile such that the computer knows where you have installed gromacs.
<![CDATA[nano .bash_profile
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I prepare to use the nano because of its more user-friendly interface compared to that vi. In the .bash_profile, please write:
<![CDATA[export PATH=/home/username/gromacs_bin/bin:$PATH
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Logout and login again, and now you can use gromacs for molecular simulation!
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