
## GROMACS 4.5.5

```
tar -zxf gromacs-4.5.5.tar.gz 
cd gromacs-4.5.5/

[4.5.5-goalf-CUDA]

module load goalf

export OPENMM_ROOT_DIR=/home/users/wjurkowski/openmm
mkdir build_gromacs_gpu
cd build_gromacs_gpu
cmake .. -DGMX_OPENMM=ON -DCMAKE_INSTALL_PREFIX=/home/users/wjurkowski/gromacs
make mdrun
make install-mdrun
```

## GROMACS 4.6

```
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz
tar -zxf gromacs-4.6.tar.gz
cd gromacs-4.6

[4.6-parallel-goalf]

module load goalf
CC=mpicc CXX=mpiCC

mkdir build_gromacs_mpi
cd build_gromacs_mpi

cmake .. -DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release  -DCMAKE_INSTALL_PREFIX=/home/users/wjurkowski/gromacs_mpi
make mdrun
make install-mdrun
cd ..
mkdir build_gromacs
cd build_gromacs
cmake .. -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release  -DCMAKE_INSTALL_PREFIX=/home/users/wjurkowski/gromacs_mpi
make
make install

[4.6-parallel-goalf-CUDA]

module load goalf
module load CUDA
CC=mpicc CXX=mpiCC

mkdir build_gromacs_gpu-mpi
cd build_gromacs_gpu-mpi

cmake .. -DGMX_OPENMP=ON -DGMX_GPU=ON -DGMX_MPI=ON -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DFFTW_INCLUDE_DIR=/opt/apps/HPCBIOS.20130301/software/FFTW/3.3.1-gompi-1.1.0-no-OFED/include \
 -DFFTW_LIBRARY=/opt/apps/HPCBIOS.20130301/software/FFTW/3.3.1-gompi-1.1.0-no-OFED/lib/libfftw3_mpi.a -DCMAKE_INSTALL_PREFIX=/home/users/wjurkowski/gromacs-gpu
make mdrun
make install-mdrun
mkdir build_gromacs
cd build_gromacs
cmake .. -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release  -DCMAKE_INSTALL_PREFIX=/home/users/wjurkowski/gromacs-gpu
make
make install

[4.6-parallel-ictce-CUDA]

module load ictce	#loads intelFFTW intelMPI intelMKL and compilers
module load CUDA
CC=mpiicc CXX=mpicxx

cd gromacs-4.6
mkdir build_gromacs_gpu_mpi
cd build_gromacs_gpu-mpi

cmake .. -DGMX_OPENMP=OFF -DGMX_GPU=OFF -DGMX_MPI=ON -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release \ 
-DCMAKE_INSTALL_PREFIX=/home/users/wjurkowski/gromacs-gpu \
-DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES="/opt/apps/HPCBIOS.20130301/software/imkl/11.0.2.146/mkl/lib/intel64/libmkl_intel_thread.a; \
/opt/apps/HPCBIOS.20130301/software/imkl/11.0.2.146/mkl/lib/intel64/libmkl_core.so; \
/opt/apps/HPCBIOS.20130301/software/imkl/11.0.2.146/mkl/lib/intel64/libmkl_em64t.a;/usr/lib64/libpthread.so" \
-DMKL_INCLUDE_DIR=/opt/apps/HPCBIOS.20130301/software/imkl/11.0.2.146/mkl/include
make mdrun
make install-mdrun
cd ..
mkdir build_gromacs
cd build_gromacs
cmake .. -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release  -DCMAKE_INSTALL_PREFIX=/home/users/wjurkowski/gromacs-gpu
make
make install

```
