Software package for simulations using the coarse-grained CALVADOS model
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arXiv
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| Hauptverfasser: | , , , , , , , , |
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| Format: | Preprint |
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2025
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| author | von Bülow, Sören Yasuda, Ikki Cao, Fan Schulze, Thea K. Trolle, Anna Ida Rauh, Arriën Symon Crehuet, Ramon Lindorff-Larsen, Kresten Tesei, Giulio |
| author_facet | von Bülow, Sören Yasuda, Ikki Cao, Fan Schulze, Thea K. Trolle, Anna Ida Rauh, Arriën Symon Crehuet, Ramon Lindorff-Larsen, Kresten Tesei, Giulio |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2504_10408 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Software package for simulations using the coarse-grained CALVADOS model von Bülow, Sören Yasuda, Ikki Cao, Fan Schulze, Thea K. Trolle, Anna Ida Rauh, Arriën Symon Crehuet, Ramon Lindorff-Larsen, Kresten Tesei, Giulio Biomolecules 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. |
| title | Software package for simulations using the coarse-grained CALVADOS model |
| topic | Biomolecules |
| url | https://arxiv.org/abs/2504.10408 |