Installation
Currently, only the development version of cg_openmm is available.
Download cg_openmm from GitHub using:
git clone https://github.com/shirtsgroup/cg_openmm.git
In the base directory of cg_openmm, install using:
python setup.py install
To use structural analysis features such as:
predicting a native structure by clustering REMD trajectories
calculating bonded distributions
you will also need to install analyze_foldamers, available through GitHub:
git clone https://github.com/shirtsgroup/analyze_foldamers.git
In the base directory of analyze_foldamers, install using:
python setup.py install
Conda environment
cg_openmm is currently tested and maintained on python 3.6, 3.7, and 3.8.
Create an anaconda environment for running cg_openmm by specifying the following dependencies:
conda create -n cg_openmm_env python=3.X mdtraj mpi4py numpy openmm openmmtools physical_validation
pymbar scikit-learn scipy
Alternatively, an environment can be created from one of the .yml files provided with cg_openmm.