Install GROMACS

• For single CPU

1.First, install FFTW library
Download FFTW 3.2.2 from http://www.fftw.org/download.html

$sudo ./configure --enable-float --enable-threads --enable-sse
$sudo make
$sudo make install

(note: --enable-float is important for install GROMACS correctly)

2. Set environment values to .bashrc file
export CPPFLAGS=-I/usr/local/include
export LDFLAGS=-L/usr/local/lib

3. Install GROMACS
Download GROMACS 4.0.7 from http://www.gromacs.org/index.php?title=Download_%26_Installation

$sudo ./configure --enable-float
$sudo make
$sudo make install

4. Set environment value for GROMACS

 # GROMACS
GROMACS=/usr/local/gromacs
export PATH=$GROMACS/bin:$PATH
export MANPATH=$GROMACS/share/man:$MANPATH
export LD_LIBRARY_PATH=$GROMACS/lib:$LD_LIBRARY_PATH
source $GROMACS/bin/GMXRC

• For parallel computation with multi-processor

1. Install lam-mpi or open mpi or mpich2
2. Set environment valuables

export PATH=/usr/lib/lam/bin:$PATH

2. Install FFTW3
$ sudo ./configure --enable-float --enable-mpi --enable-sse
$sudo make
$sudo make install

3. Set environment valuables of FFTW3 for GROMACS

export CPPFLAGS="-I/usr/local/include -I/home/liuxi/apps/openmpi/include -I/home/liuxi/apps/openmpi/lib -I/usr/lib/lam/lib -I/usr/lib/lam/include"
export LDFLAGS=-L/usr/local/lib

4. Install GROMACS
$sudo ./configure --prefix=/home/xxxx/apps/gromacs --enable-mpi --enable-float --program-suffix="_mpi"
$sudo make
$sudo make install

5. Set environment valuable

# GROMACS

GROMACS=/usr/local/gromacs
export PATH=$GROMACS/bin:$PATH
export MANPATH=$GROMACS/share/man:$MANPATH
export LD_LIBRARY_PATH=$GROMACS/lib:$LD_LIBRARY_PATH
source $GROMACS/bin/GMXRC


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Some useful links:
http://lists.gromacs.org/pipermail/gmx-users/2008-April/033406.html
http://www.mail-archive.com/gmx-users@gromacs.org/msg27951.html
http://youyong.zz23.com/html/keyangongju/2010/0128/38529.html
http://www.mdbbs.org/thread-18939-1-2.html