A  Suite of Tutorials for the BioSimSpace Framework for Interoperable Biomolecular Simulation [Article v1.0]

Lester O. Hedges; Sofia Bariami; Matthew Burman; Finlay Clark; Benjamin P. Cossins; Adele Hardie; Anna M. Herz; Dominykas Lukauskis; Antonia S. J. S.  Mey; Julien Michel; Jenke Scheen; Miroslav Suruzhon; Christopher J. Woods; Zhiyi Wu

doi:10.33011/livecoms.5.1.2375

Authors

Lester O. Hedges Advanced Computing Research Centre, University of Bristol, UK and OpenBioSim Community Interest Company, UK https://orcid.org/0000-0002-5624-0500
Sofia Bariami EaStCHEM School of Chemistry, University of Edinburgh, UK https://orcid.org/0000-0002-5240-7684
Matthew Burman OpenBioSim Community Interest Company, UK https://orcid.org/0000-0001-5360-0024
Finlay Clark EaStCHEM School of Chemistry, University of Edinburgh, UK https://orcid.org/0000-0003-0474-5475
Benjamin P. Cossins Exscientia Plc., Oxford, UK https://orcid.org/0000-0002-6699-8833
Adele Hardie EaStCHEM School of Chemistry, University of Edinburgh, UK https://orcid.org/0009-0002-9943-9920
Anna M. Herz EaStCHEM School of Chemistry, University of Edinburgh, UK https://orcid.org/0000-0003-2831-6691
Dominykas Lukauskis Department of Chemistry and Institute of Structural and Molecular Biology, University College London, UK https://orcid.org/0000-0002-4999-2691
Antonia S. J. S. Mey EaStCHEM School of Chemistry, University of Edinburgh, UK https://orcid.org/0000-0001-7512-5252
Julien Michel EaStCHEM School of Chemistry, University of Edinburgh, UK and OpenBioSim Community Interest Company, UK https://orcid.org/0000-0003-0360-1760
Jenke Scheen EaStCHEM School of Chemistry, University of Edinburgh, UK https://orcid.org/0000-0001-9781-0445
Miroslav Suruzhon Exscientia Plc., Oxford, UK https://orcid.org/0000-0002-6794-1679
Christopher J. Woods Advanced Computing Research Centre, University of Bristol, UK https://orcid.org/0000-0001-6563-9903
Zhiyi Wu Exscientia Plc., Oxford, UK https://orcid.org/0000-0002-7615-7851

DOI:

https://doi.org/10.33011/livecoms.5.1.2375

Keywords:

molecular dynamics, interoperability, metadynamics, steered MD, alchemical free energy

Abstract

This tutorial serves as a getting-started guide for BioSimSpace (BSS), an interoperable molecular simulation framework, that allows simulations with different sets of molecular dynamics software packages. This tutorial will cover four main use cases for BioSimSpace. The introductory tutorial introduces the basic structure of BioSimSpace, how to use the API to access functionality, and how to write code for setting up and running standard molecular dynamics simulations. Three advanced use cases of BSS are then provided, describing how to set up and run a funnel metady- namics simulation, steered molecular dynamics, and relative or absolute alchemical binding free energy calculations.

A Suite of Tutorials for the BioSimSpace Framework for Interoperable Biomolecular Simulation [Article v1.0]

Authors

DOI:

Keywords:

Abstract

Downloads

Published

How to Cite

Issue

Section

Categories

License

Information

Browse

browsebyissue

twitterfeed