Introduction

The COSMO model is a Python library that offers flexibility to set up coarse-grained simulation of IDP using the MD framework of OpenMM toolkit. The codebase is based on sbmOpenMM scripts. It automates the creation of openmm.system classes that contain the necessary force field parameters to run molecular dynamics simulations using a protein structure as the only necessary inputs.

COSMO is divided in four main classes:

  1. system

  2. models

  3. engine (the simulation runner; see Running simulations)

  4. geometry

system, is the main class that holds all the methods to define, modify and create CG system to be simulated with OpenMM. Class inheritance from openmm.system with some more attributes for COSMO.

models, class contains set of models, each model contains a collection of sequence of commands to build model, allows to easily set up CG models.

engine (with cosmo.read_simulation_config and the cosmo-mdrun runner) reads the parameter controls, builds the model and runs the simulation.

geometry, contains methods to calculate the geometrical parameters from the input structures. It’s not useful in current need of simulation method.

The library is open-source and offers flexibility to simulate IDPs.