1. download source code:
git clone git://git.gromacs.org/gromacs.git

2. install openMM and CUDA library into

/soft/gromacs-gpu/openmm (download from https://simtk.org/project/xml/downloads.xml?group_id=506 )
/soft/gromacs-gpu/cuda

configuring .cshrc as following

etenv OPENMM_ROOT_DIR /soft/openmm
setenv LD_LIBRARY_PATH /soft/gromacs4.6-gpu/cuda/lib64:/soft/gromacs4.6-gpu/cuda/lib:/soft/gromacs-gpu /openmm/lib

3. compile GROMACS CUDA from source code
mkdir cuda
cd cuda
cmake ../. -DGMX_OPENMM=ON -DGMX_THREADS=OFF -DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6-gpu
make -j24
make install

4. configure .cshrc
source /soft/gromacs4.6-gpu/bin/GMXRC.csh

done!







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