Having said that, I never ended up using the GPU-enabled gromacs for which I built openmm, so it was all an enormous waste of time -- for those of you thinking about GPU/Gromacs know this:
* not all graphics cards are supported or worth supporting
* there's no speed-up for explicit solvent molecules, and what else would you use gromacs or MD for?
* consumer-grade graphics cards get very hot
I make no attempt at ferreting out what packages are needed other than what I'm explicitly prompted for. Look at http://verahill.blogspot.com.au/2012/01/debian-testing-64-wheezy_20.html for an indication of what you might need.
Also, I already have openmm 4.0 installed, so e.g. paths and other things defined in the post above are still active.
Start here
Register with simtk.org and download the source file.
sudo apt-get install cmake-curses-gui libgccxml-dev gccxml nvidia-cuda-toolkit
unzip -x OpenMM4.1-Source.zipe
mkdir openmm_build
cd openmm_build/
ccmake -i ../OpenMM4.1-Source/
It'll say Empty Cache. Hit c which will populate the list.
I think we can ignore the EMU libs since they do device emulation. I never figured out what the CUT program was and it's not mentioned in the manual from what I can see.
These are the settings I chose -- I had problems before setting the OPENCL parts (in red) to off.
BUILD_TESTING:BOOL=ON
CMAKE_BUILD_TYPE:STRING=Release
CMAKE_INSTALL_PREFIX:PATH=/home/verahill/.openmm
CUDA_BUILD_TYPE:STRING=Device
CUDA_INSTALL_PREFIX:PATH=/usr/bin
CUDA_NVCC:FILEPATH=/usr/bin/nvcc
DL_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libdl.so
FOUND_CUBLAS:FILEPATH=/usr/lib/x86_64-linux-gnu/libcublas.so
FOUND_CUBLASEMU:FILEPATH=FOUND_CUBLASEMU-NOTFOUND
FOUND_CUFFT:FILEPATH=/usr/lib/x86_64-linux-gnu/libcufft.so
FOUND_CUFFTEMU:FILEPATH=FOUND_CUFFTEMU-NOTFOUND
FOUND_CUT:FILEPATH=FOUND_CUT-NOTFOUND
FOUND_CUT_INCLUDE:PATH=FOUND_CUT_INCLUDE-NOTFOUND
GCCXML_EXTRA_ARGS:STRING=
GCCXML_PATH:FILEPATH=/usr/bin/gccxml
OPENMM_BUILD_AMOEBA_CUDA_LIB:BOOL=ON
OPENMM_BUILD_AMOEBA_PLUGIN:BOOL=ON
OPENMM_BUILD_CUDA_LIB:BOOL=ON
OPENMM_BUILD_CUDA_TESTS:BOOL=TRUE
OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS:BOOL=ON
OPENMM_BUILD_FREE_ENERGY_CUDA_LIB:BOOL=ON
OPENMM_BUILD_FREE_ENERGY_PLUGIN:BOOL=ON
OPENMM_BUILD_OPENCL_LIB:BOOL=OFF
OPENMM_BUILD_OPENCL_TESTS:BOOL=OFF
OPENMM_BUILD_PYTHON_WRAPPERS:BOOL=ON
OPENMM_BUILD_RPMD_OPENCL_LIB:BOOL=OFF
OPENMM_BUILD_RPMD_PLUGIN:BOOL=ON
OPENMM_BUILD_SERIALIZATION_SUPPORT:BOOL=ON
OPENMM_BUILD_STATIC_LIB:BOOL=ON
OPENMM_GENERATE_API_DOCS:BOOL=OFF
OPENMM_SVN_REVISION:STRING=exported
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python
SVNVERSION_PROGRAM:FILEPATH=/usr/bin/svnversion
SWIG_EXECUTABLE:FILEPATH=/usr/bin/swig
SWIG_VERSION:STRING=2.0.7
Make your changes and hit c again, then hit g which brings you back to the terminal.
make -d|tee make.log
make test
If all goes well you'll see
126/126 Test #126: TestParser ...................................... Passed 0.02 sec
100% tests passed, 0 tests failed out of 126
Total Test time (real) = 345.83 sec
make install
[..]
-- Installing: /home/verahill/.openmm/examples/Makefile
-- Installing: /home/verahill/.openmm/examples/NMakefile
-- Installing: /home/verahill/.openmm/examples/MakefileNotes.txt
-- Installing: /home/verahill/.openmm/examples/Empty.cpp
And you are done!
tree ~/.openmm/ -L 4 -d
.openmm/
|-- bin
|-- docs
| |-- api-c++
| `-- api-python
|-- examples
| `-- VisualStudio
|-- include
| `-- openmm
| |-- internal
| `-- serialization
|-- lib
| `-- plugins
`-- licenses
