Installation of dependencies
It is so important to go through the installation procedures illustrated on this webpage as this makes sure that the installations of other GNU/Linux software, such as gromacs, go smoothly without any error. Also, you have to make sure you compile everything with the same version of gfortran.
Installation of FFTW3 for Gromacs-5.1.4
First, you need to download the fftw3.tar.gz folder from FFTW homepage and run the following command:
<![CDATA[tar -xzvf fftw-3.3.6-pl1.tar.gz
mkdir fftw_bin
cd fftw-3.3.6-pl1
]]>
After that, you have to configure it so carefully with the suitable threads and proceed to installation.
<![CDATA[./configure --enable-float --enable-shared --prefix=/home/username/.../path/to/fftw_bin
make prefix=/home/username/.../path/to/fftw_bin
make install prefix=/home/username/.../path/to/fftw_bin/bin
]]>
Finally, please go ahead to edit the .bash_profile using nano. In my opinion, nano is more user friendly than that of vi.
<![CDATA[nano .bash_profile]]>
Add the following line to the .bash_profile:
<![CDATA[export PATH=/home/username/.../path/to/fftw_bin:$PATH]]>
Now, logout and login again. Thing should work perfectly.
Installation of cmake
It is basically the same as what we have done for the installation of FFTW3 library. First, you need to download the cmake-3.8.0-rc1.tar.gz folder from here and run the following command:
<![CDATA[tar -xzvf cmake-3.8.0-rc1.tar.gz
mkdir cmake_bin
cd cmake-3.8.0-rc1
./cofigure --prefix=/home/username/.../path/to/cmake_bin
make prefix=/home/username/.../path/to/cmake_bin
make install prefix=/home/username/.../path/to/cmake_bin
]]>
Again, please remember to include the path in the .bash_profile. Logout and login again to make stuff work.
Installation of MPI for Gromacs-5.1.4
You will need to download openmpi-2.0.2.tar.gz from here. After that, go ahead to run the following command:
<![CDATA[tar -xzvf openmpi-2.0.2.tar.gz
mkdir mpi_bin
cd openmpi-2.0.2
./configure --prefix=/home/username/.../path/to/mpi_bin
make prefix=/home/username/.../path/to/mpi_bin
make install prefix=/home/username/.../path/to/mpi_bin]]>
If you have gone through the installation of other dependencies, you should have a very clear idea how to include the path in .bash_profile.
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