Software package for simulations using the coarse-grained CALVADOS model
Sören von Bülow, Ikki Yasuda, Fan Cao, Thea K. Schulze, Anna Ida Trolle, Arriën Symon Rauh, Ramon Crehuet, Kresten Lindorff-Larsen, Giulio Tesei
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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.