4 Notes
- CUDA platform on GPU workstation—This latest version of
WATsite relies on OpenMM accelerated MD simulation, but a
previous version, WATsite2.0, based on Gromacs simulations is
available in case a GPU workstation is not available. The
WATsite-compatible OpenMM has to be compiled in order
to perform MD simulation and generate water interaction
energies for later analysis. The source code is located in the
openmm-watsitefolder, and the user can follow the standard
OpenMM compilation steps. Here, we will briefly list the steps.
(a) Download CUDA 8.0 and install both the drivers and
CUDA toolkit. Set the environment variable accordingly
before compilation. We provide an example below:
export PATH¼$PATH:/usr/local/cuda-8.0/bin/
export LD_LIBRARY_PATH¼/usr/local/cuda-8.0/lib64:
$LD_LIBRARY_PATH
export CUDA_HOME¼/usr/local/cuda-8.0/
export OPENMM_CUDA_COMPILER¼/usr/local/
cuda-8.0/bin/nvcc
(b) Go to the Openmm-watsite directory, make a new direc-
tory and change into the directory.
(c) Configure with ccmake:
ccmake ../
(d) Configure(“c”).
(e) Set the variable CMAKE_INSTALL_PREFIX to the loca-
tion where you want to install OpenMM.
(f) Set the variable PYTHON_EXECUTABLE to the Python
interpreter you plan to use OpenMM with.
(g) Configure (press “c”) again.
(h) Generate (“g”) the Makefile.
(i) Start the installation by the following command: (if the
location of installation is not a system area, sudo is not
required)
(sudo) make install && (sudo) make PythonInstall
(j) Verify your installation by the following command:
python -m simtk.testInstallation
Before starting the OpenMM simulation instep 4, the user
needs to make sure the environment variables for CUDA in
(a) are set correctly. Depending on the number of GPU cards
available, the user can spread multiple jobs by specifying the
device index instep 3. - Protonation states —Protonation states for ionizable residues
in the protein binding site may significantly affect the
Calculation of Water Thermodynamics 399