cg_openmm is a python package for setup and thermodynamic analysis of coarse-grained foldamer replica exchange molecular dynamics simulations run using OpenMM.
For further details refer to the web-based documentation: https://cg-openmm.readthedocs.io/en/latest/
Cite:
Walker, CC; Meek, GA; Fobe, TL; Shirts, MR. Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure. J. Chem. Theory Comput. 2021, 17 (10), 6018–6035. https://doi.org/10.1021/acs.jctc.1c00528
To install cg_openmm, run python setup.py install in the base directory.
To use structural analysis features, including native structure determination and calculation of bonded distributions, also install analyze_foldamers.
mdtraj | mpi4py | numpy | openmm | openmmtools | physical_validation | pymbar | scikit-learn | scipy
To test your installation, open a new Python session and type the command import cg_openmm.