cg_openmm

cg_openmm is a Python package for setup and thermodynamic analysis of coarse-grained oligomer replica exchange molecular dynamics (REMD) simulations, with a focus on identifying and analyzing cooperative folding transitions.

• Build coarse-grained hetero-oligomer topology and force field definitions using the highly customizable potentials in OpenMM

• Set up GPU-accelerated REMD simulations with a CGModel and a few lines of python code

• Compute heat capacity as a near-continuous function of temperature using MBAR and a bootstrapping scheme

• Compute native contact fraction expectation and free energy of folding as functions of temperature using MBAR and a bootstrapping scheme (requires a native structure determined using analyze_foldamers)

• Predict helix-stabilizing force field parameters using a helical geometry optimization tool

User Guide

• Installation
  • Conda environment
• Examples
  • Creating a cgmodel
  • Replica exchange MD simulations
  • Calculating heat capacity

API documentation:

• Build module
• CGModel class
• Ensembles module
• Parameters module
• Simulation module
• Thermo module
• Utilities module

Indices and tables

• Index

• Module Index

• Search Page