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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, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. source

HPCAC Guide http://www.hpcadvisorycouncil.com/pdf/GROMACS_Best_Practices.pdf
Acceleration and parallelization http://www.gromacs.org/Documentation/Acceleration_and_parallelization

cd ~
mkdir GROMACS
cd GROMACS

Create a source file:

vim bashrc

source /data/opt/intel/bin/compilervars.sh intel64
source /data/opt/intel/mkl/bin/mklvars.sh intel64
export PATH=/data/opt/openmpi-1.8.7-ics2013/bin:$PATH
export LD_LIBRARY_PATH=/data/opt/openmpi-1.8.7-ics2013/lib:$LD_LIBRARY_PATH
export PATH=/home/$USER/GROMACS/libs/binutils/bin:$PATH
export LD_LIBRARY_PATH=/home/$USER/GROMACS/libs/binutils/lib:$LD_LIBRARY_PATH
export PATH=/home/$USER/GROMACS/libs/cmake/bin:$PATH
export CC=icc
export CXX=icpc
export CFLAGS='-O3'
export CXXFLAGS='-O3'
export F77=ifort
export FC=ifort
export F90=ifort
export FFLAGS='-O3'
export CPP='icc -E'
export CXXCPP='icpc -E'

source bashrc

mkdir tars
mkidr libs
mkdir tests
cd tars

Install dependencies from repository:

sudo yum install blas-devel lapack-devel atlas-devel libxml2-devel

cd ~/GROMACS/tars
wget http://www.cmake.org/files/v3.0/cmake-3.0.2.tar.gz
tar -xf cmake-3.0.2.tar.gz
cd cmake-3.0.2
./configure --prefix=/home/$USER/GROMACS/libs/cmake
make -j4
make install

cd ~/GROMACS/tars
wget https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.gz
tar -xf binutils-2.25.tar.gz
cd binutils-2.25
./configure --prefix=/home/$USER/GROMACS/libs/binutils
make -j4
make install

cd ~/GROMACS/tars
wget https://kth.box.com/shared/static/7uwctwj33h4uo2f8d1tmdyj9afaj3hzy.gz
tar -xf 7uwctwj33h4uo2f8d1tmdyj9afaj3hzy.gz
cd gromacs-5.0.6
mkdir build
cd build

cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_GPU=off -DGMX_MPI=on -DGMX_SIMD=AVX2_256 -DCMAKE_INSTALL_PREFIX=/home/$USER/GROMACS/gromacs-x86/ -DGMX_BUILD_OWN_FFTW=ON -DGMX_BUILD_UNITTESTS=ON
make -j10
make install

The CUDA version requires a CUDA SDK of at least version 4.0, however the latest is recommended (version 7.0 was used for testing). If the SDK in not found in the default /usr/local/cuda directory, then source it.

cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_GPU=on -DGMX_MPI=on -DGMX_SIMD=AVX2_256 -DCMAKE_INSTALL_PREFIX=/home/$USER/GROMACS/gromacs-cuda/ -DGMX_BUILD_UNITTESTS=ON
make -j10
make install

Source the GROMACS installation:

export PATH=/home/$USER/GROMACS/gromacs-x86/bin:$PATH

Test the installation by using the regression tests which ship with the release, available here: regressiontests.tar.gz

cd ~/GROMACS/tests
tar -xf Regressiontests.tar.gz
cd regressiontests
./gmxtest.pl -suffix _mpi all