A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
|
|
|
|
# Install the requirements
|
|
|
|
|
pip install ase pymatgen gmxscript prettytable acpype MDAnalysis
|
|
|
|
|
sudo apt install -y cmake
|
|
|
|
|
sudo apt install -y libblas-dev
|
|
|
|
|
sudo apt install -y libarpack2-dev
|
|
|
|
|
sudo apt install -y openbabel
|
|
|
|
|
# Make the bashrc
|
|
|
|
|
## Merging the Python libraries of CMMDE
|
|
|
|
|
echo "export PYTHONPATH=`pwd`/lib:$PYTHONPATH" >> ~/.bashrc
|
|
|
|
|
## Merging the CMMDE binaries to your PATH
|
|
|
|
|
echo "export PATH=`pwd`/bin:$PATH" >> ~/.bashrc
|
|
|
|
|
echo "export ORCA_COMMAND=/opt/orca/orca" >> ~/.bashrc
|
|
|
|
|
echo "export XTB_COMMAND=/usr/local/bin/xtb" >> ~/.bashrc
|
|
|
|
|
# PATH to DCDFTBMD program, please refer the README.md to register the program at Nakai Lab of Waseda University
|
|
|
|
|
#echo "export DCDFTB_COMMAND=/path/to/DCDFTBMD/bin/binary" >> ~/.bashrc
|
|
|
|
|
# If you have GROMACS
|
|
|
|
|
#echo "export GROMACS_COMMAND=`pwd`/lib/cmmde_solution.py" >> ~/.bashrc
|
|
|
|
|
source ~/.bashrc
|
