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Molecular Dynamics

Installing Gromacs
  1. Get the latest version of your compiler.

  2. Check you have CMake version 2.8.x or later.

  3. Unpack the GROMACS tarball.

  4. Make a separate build directory and change to it.

  5. Run CMake with the path to the source as an argument

  6. Run make and make install

Or, as a sequence of commands to execute:

tar xfz gromacs-4.6.1.tar.gz
cd gromacs-4.6.1
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON
make
sudo make install

This will download and build first the prerequisite FFT library followed by GROMACS. If you already have FFTW installed, you can remove that argument to cmake. Overall, this build of GROMACS will be correct and reasonably fast on the machine upon which CMake ran. It will generally be 30-50% faster than GROMACS 4.5.x, but if you want to get the maximum value for your hardware with GROMACS, you'll have to read further. Sadly, the interactions of hardware, libraries, and compilers are only going to continue to get more complex.



Install CUDA tool kit

http://www.codeproject.com/Articles/513265/GPU-Computing-Using-CUDA-Eclipse-and-Java-with-JCu

http://comecodewithus.blogspot.tw/2012/11/these-notes-are-based-on-these-notes.html


/home/davince/Downloads

cuda-samples-linux-5.5.22-16488124.run

cuda-linux64-rel-5.5.22-16488124.run

NVIDIA-Linux-x86_64-319.37.run


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