Building GROMACS

This file documents the use of the x86 Open64 Compiler Suite.
© 2009 Advanced Micro Devices, Inc.


GROMACS is a molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. To build GROMACS, you will need the source for GROMACS, along with the FFTW software. The steps for configuring and building each of these codes, and any known limitations, are described in the sections below.

Download: GROMACS (version 3.2.1).

Download: FFTW (version 2.1.5).

Building GROMACS

Follow these steps to build GROMACS. The following commands will default to directories in your home directory, though you can set them to wherever you wish to install GROMACS.

Step 1, FFTW: see build_fftw.

Step 2, GROMACS:

     >mkdir ~/gromacs
     >cd ~/gromacs
     >mkdir src
     >cd src
     >export MY_FFTW_PATH=~/fftw
     >export MY_GROMACS_PATH=~/gromacs
     >tar zxvf gromacs-3.3.3.tar.gz
     >cd gromacs-3.3.3/
     >export CC=opencc CFLAGS="-O3 -OPT:Ofast" \
      CPPFLAGS=-I$MY_FFTW_PATH/include \
     >./configure --prefix=$MY_GROMACS_PATH
     >make install

Known Limitations

There are no known limitations