cg_openmm
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/
Installation
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.
Dependencies:
mdtraj | mpi4py | numpy | openmm | openmmtools | physical_validation | pymbar | scikit-learn | scipy
Testing your installation:
To test your installation, open a new Python session and type the command import cg_openmm
.