Repositories

The OpenMM modifications are at https://simtk.org/home/nmlopenmm/ and modified Protomol at https://simtk.org/home/protomol/.

To get the code

svn checkout https://simtk.org/svn/nmlopenmm nmlopenmm
svn checkout https://simtk.org/svn/protomol nmlprotomol

Mac OSX environment

#OpenMM/Cuda
export OPENMM_HOME=/Users/chrissweet/Protomol/openmmlib/
export "DYLD_LIBRARY_PATH=$OPENMM_HOME/lib:$DYLD_LIBRARY_PATH:/Developer/GPU Computing/C/lib"
export CUDA_HOME=/usr/local/cuda
export LIBRARY_PATH=/Developer/GPU\ Computing/C/common/lib/darwin/:/Developer/GPU\ Computing/C/lib/:$LIBRARY_PATH

Compiling OpenMM

Check CUDA first! For Max OSx

cd "/Developer/GPU Computing/C/bin/darwin/release"
./deviceQuery

In the OpenMM directory run

ccmake CMakeLists.txt

then c to configure, update library directory to /Users/chrissweet/Protomol/openmmlib/, update OPENMM_BUILD_CUDA_LIB to ON, c again then g to write it out.

Then run

cmake CMakeLists.txt
make
make install

Compiling Protomol

Run

scons gui=1 lapack=1 openmm=cuda (or reference)

Test OpenMM and Protomol

You can test the OpenMM libraries in its directory with

./TestCudaRandom

To test protomol with CUDA in models/alanineamber/

ProtoMol-app gbndomm.conf

More about gbndomm.conf

Code

Input files used for testing/development

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