Software package for simulations using the coarse-grained CALVADOS model

TL;DR

The paper introduces the CALVADOS software package that facilitates biomolecular simulations using a coarse-grained model, enabling analysis of diverse biomolecular systems with an open-source, extendable framework.

Contribution

It provides a new, user-friendly software package for CALVADOS model simulations, including design, implementation, and example usage instructions.

Findings

Eases simulation of various biomolecules with CALVADOS models

Open-source and extendable software architecture

Supports analysis of disordered proteins and RNA in crowded environments

Abstract

We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS models of biomolecules including disordered proteins, multi-domain proteins, proteins in crowded environments, and disordered RNA. We briefly describe the CALVADOS force fields and how they were parametrised. We then discuss the design paradigms and architecture of the CALVADOS package, and give examples of how to use it for running and analysing simulations. The simulation package is freely available under a GNU GPL license; therefore, it can easily be extended and we provide some examples of how this might be done.