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cg_openmm

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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.

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Tools to build coarse grained models and perform simulations with OpenMM

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