Introduction

The hpsOpenMM 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.

hpsOpenMM is divided in four main classes:

1. system

2. models

3. dynamics

4. geometry

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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 hpsOpenMM.

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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.

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dynamics class auto read the parameter controls, build the model and run simulation.

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

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