tar xfz gromacs-5.1.tar.gz
cd gromacs-5.1
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON  -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=on (-DCMAKE_INSTALL_PREFIX=/../../path to the desitination)
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

4.6.4(on sun):

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=on -DGMX_GPU=OFF

4.6.7(on cluster)

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/export/apps/gromacs4.6.7

 

Install 4.5.7

install fftw:

./configure --enable-shared --enable-float --prefix=/home/zwei/softwares/fftw334 --with-pic

tar -xvzf gromacs-4.5.7.tar.gz

cd gromacs-4.5.7

./configure

make

 

http://www.gromacs.org/Documentation/Installation_Instructions/Cmake

Starting with the 4.5 release, it is possible to configure and compile the source code with it. With the 4.6 release CMake is the deafult and only build system, while autoconf/automake is deprecated. The information below pertains to the way GROMACS 4.5.x used CMake

$ tar xvfz gromacs-src.tar.gz
$ ls
gromacs-src
cd gromacs-src
$ mkdir build
$ cd build
$ CMAKE_PREFIX_PATH=/home/zwei/softwares/fftw334 cmake ../
$sudo make install

Steps to Perform a Simulation
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

 

 

This is the installation of Gromacs 3.1 for constant pH simulation

unpack fftw, install by

./configure --enable-threads --enable-float --prefix=/home/zwei/softwares/fftw-3.3.4

make

make install

install gromacs by

./configure --prefix=/home/zwei/work/MD/constant_pH_gromacs/gromacs_3.3.1_cphmd_v1.3

make

sudo make install

INSTALL CUDA SUPPORTED GROMACS 5

unsupported GNU version! gcc versions later than 4.9 are not supported!

fix:

Patch the host_config.h header file
CUDA 7 is not officially supported for gcc compilers with version greater than 4.9. If at this point you tried to build some of the cuda samples you would be greeted with;

In file included from /usr/local/cuda-7.0/bin/..//include/cuda_runtime.h:62:0,
from :0:
/usr/local/cuda-7.0/bin/..//include/host_config.h:105:2: error: #error -- unsupported GNU version! gcc 4.10 and up are not supported!
#error -- unsupported GNU version! gcc 4.10 and up are not supported!
Of course you get that error because we are running gcc 5.1. Lets fix that … we are just going to ignore the error and build stuff anyway!

Edit the file referred to in the error

/usr/local/cuda-7.0/include/host_config.h
#if __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 9)
//#error -- unsupported GNU version! gcc 4.10 and up are not supported!
#endif /* __GNUC__> 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 9) */

 

Install gromacs on xeon

mkdir build

cd build

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/zwei/softwares/gromacs_5.1.2

make -j 12
make check
make install

 

Install gromacs 2016-3 on xeon with gpu support

CC=mpicc CXX=mpicxx cmake ../ -DGMX_OPENMP=ON -DGMX_GPU=ON -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/home/zwei/softwares/gromacs_2016_3 -DGMX_MPI=ON -DGMX_X11=on

make -j 12

make check

make install

gmx_mpi mdrun -resethway -noconfout -deffnm dppc-md -v -pin on -nb gpu

5.1.4(on fock)

cmake ../ -DGMX_OPENMP=ON -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/export/apps/gromacs_5.1.4 -DGMX_MPI=ON -DGMX_SIMD=AVX_256