This is a package for building atomic-level systems supercell lattices, energy minimizing supercell lattices, running MD simulations of supercell lattices and analysis of the simulations.
git clone https://github.com/wutobias/xtalmd-scripts
Setup a conda environment to get the dependencies right with xtalmd.yml:
conda env create -f xtalmd.yml
Activate it:
conda activate xtalmd
If you want to run energy minimizations or lattice simulations, also install the package ray:
pip install ray['default']
python setup.py install
Almost all dependencies should be covered in the xtalmd.yml file. All other dependencies are listed below.
We make heavy usage of xyz2mol, which is developed in the Jensen group and can be found here.
In order to be able to use the cgenff CHARMM force field, the programs cgenff and charmm must be in PATH. We recommend using cgenff version 2.5.1 and charmm version 46b1, both can be obtained free of charge for academic users.
The force field files for CgenFF should be obtained here.
The program BOSS must be installed and available in PATH in order to use this force field. Make sure that the environment variable BOSSdir is set and points to the directory of the BOSS installation. The BOSS program is available for free here. After that install the program ligpargen from here.
Some of the optional system building routines can only be used together with OpenEye toolkit, which requires a license.
A bunch of examples for the different things this package can do, have a look at the examples.
Tobias Hüfner (UC San Diego)