In this section we describe the process that we went through in order to get the molecular dynamics program Gromacs up and running on Mac OS X.
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As Gromacs is relying on the FFTW C subroutine library for computing discrete Fourier transforms, we need to have these installed. Download FFTW 3.1.1 and save into the ~/Downloads/ directory. Then unpack into the /usr/local/src directory and install:
> cd /usr/local/src > tar -xvf ~/Downloads/fftw-3.3.1.tar.gz > cd fftw-3.3.1 > ./configure --enable-threads --enable-float > make > sudo make install
This latter command asks for a root password that you should provide. This installation process installs the FFTW header files in /usr/local/include and the library files in /usr/local/lib.
Download cmake 2.8.6 and follow the installation instructions (make sure to install the command-line links). Check the installation:
> which cmake /usr/bin/cmake > cmake --version cmake version 2.8.6
If you have HomeBrew installed, you could try this instead:
> brew install cmake
Download and unpack gromacs 4.5.5. In our case, we have downloaded into the ~/Downloads directory and are unpacking into the /usr/local/src/ directory:
> cd /usr/local/src > tar -xvf ~/Downloads/gromacs-4.5.5.tar.gz > cd gromacs-4.5.5 > mkdir build > cd build > cmake .. > make > sudo make install
The latter command installs all Gromacs-related files in their respective directories:
> HTML-documentation: /usr/local/gromacs/share/gromacs/html > Topology and forcefield files: /usr/local/gromacs/share/gromacs/top > Include files: /usr/local/gromacs/include/gromacs > Libraries: /usr/local/gromacs/lib > Binaries: /usr/local/gromacs/bin
The last thing to do is to set the paths correctly. This is done by appending the following command to your ~/.bash_profile file:
> echo "source /usr/local/gromacs/bin/GMXRC" >> ~/.bash_profile
In a new shell window, you can now test the installation:
> mdrun -version :-) G R O M A C S (-: Giving Russians Opium May Alter Current Situation :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: Program: mdrun Version: VERSION 4.5.5 Precision: single Parallellization: thread_mpi FFT Library: fftw3