Compiling and Installing Gromacs 4.6.2 with OpenMPI and Intel on CentOS

Step 1: Compiling cmake To compile Gromacs 4.6.2, first you need to compile cmake 2.8 and above. At this point in writing, the current version is cmake 2.8.11.2

# tar -zxvf cmake-2.8.11.2.tar.gz
# cd cmake-2.8.11.2
# ./configure --prefix=/usr/local/cmake-2.8.11.2
# make
# make install

Step 2: Installing OpenMPI
See Blog Entry Building OpenMPI with Intel Compilers

Step 3: Installing FFTW (Single and Double Precision) 
See Blog Entry Compiling and installing FFTW 3.3.3.  

Step 4: Compiling Gromacs 4.6.2 (Single-Precision with Intel and OpenMPI)

# tar -zxvf gromacs-4.6.2.tar.gz
# cd gromacs-4.6.2
# mkdir build-cmake
# cd build-cmake
# CC=icc CMAKE_PREFIX_PATH=/usr/local/fftw-3.3.3-single/ /usr/local/cmake-2.8.11.2/bin/cmake .. 
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-4.6.2-single-intel -DGMX_X11=OFF -DGMX_MPI=ON 
-DGMX_PREFER_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF
# make
# make install

Step 5: Compiling Gromacs 4.6.2 (Double Precision with Intel and OpenMPI)

# tar -zxvf gromacs-4.6.2.tar.gz
# cd gromacs-4.6.2
# mkdir build-cmake
# cd build-cmake
# CC=icc CMAKE_PREFIX_PATH=/usr/local/fftw-3.3.3-single/ /usr/local/cmake-2.8.11.2/bin/cmake .. 
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-4.6.2-single-intel -DGMX_X11=OFF -DGMX_MPI=ON 
-DGMX_PREFER_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF -DGMX_DOUBLE=ON# make
# make install

For more information,

1. Compiling Gromacs 4.6 and PLUMED from Source
2. Gromacs Installation instructions