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

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

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

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.

Original language	English
Journal	Living Journal of Computational Molecular Science
Volume	5
Issue number	1
Early online date	14 Dec 2023
DOIs	https://doi.org/10.33011/livecoms.5.1.2375
Publication status	E-pub ahead of print - 14 Dec 2023

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10.33011/livecoms.5.1.2375

20231214MichelLivecomsVoRFinal published version, 7.23 MBLicence: Creative Commons: Attribution (CC-BY)

https://livecomsjournal.org/index.php/livecoms/article/view/v5i1e2375

EPSRC Flagship Software - BioSimSpace A shared space for the community development of biomolecular simulation workflows
Michel, J.
EPSRC
7/08/17 → 6/02/20
Project: Research

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Hedges, L. O., Bariami, S., Burman, M., Clark, F., Cossins, B. P., Hardie, A., Herz, A. M., Lukauskis, D., Mey, A. S. J. S., Michel, J., Scheen, J., Suruzhon, M., Woods, C. J., & Wu, Z. (2023). A Suite of Tutorials for the BioSimSpace Framework for Interoperable Biomolecular Simulation [Article v1.0]. Living Journal of Computational Molecular Science, 5(1). Advance online publication. https://doi.org/10.33011/livecoms.5.1.2375

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

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.",

author = "Hedges, {Lester o.} and Sofia Bariami and Matthew Burman and Finlay Clark and Cossins, {Benjamin p.} and Adele Hardie and Herz, {Anna m.} and Dominykas Lukauskis and Mey, {Antonia s. j. s.} and Julien Michel and Jenke Scheen and Miroslav Suruzhon and Woods, {Christopher j.} and Zhiyi Wu",

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month = dec,

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doi = "10.33011/livecoms.5.1.2375",

language = "English",

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Hedges, LO, Bariami, S, Burman, M, Clark, F, Cossins, BP, Hardie, A, Herz, AM, Lukauskis, D, Mey, ASJS , Michel, J, Scheen, J, Suruzhon, M, Woods, CJ & Wu, Z 2023, 'A Suite of Tutorials for the BioSimSpace Framework for Interoperable Biomolecular Simulation [Article v1.0]', Living Journal of Computational Molecular Science, vol. 5, no. 1. https://doi.org/10.33011/livecoms.5.1.2375

TY - JOUR

T1 - A Suite of Tutorials for the BioSimSpace Framework for Interoperable Biomolecular Simulation [Article v1.0]

AU - Hedges, Lester o.

AU - Bariami, Sofia

AU - Burman, Matthew

AU - Clark, Finlay

AU - Cossins, Benjamin p.

AU - Hardie, Adele

AU - Herz, Anna m.

AU - Lukauskis, Dominykas

AU - Mey, Antonia s. j. s.

AU - Michel, Julien

AU - Scheen, Jenke

AU - Suruzhon, Miroslav

AU - Woods, Christopher j.

AU - Wu, Zhiyi

PY - 2023/12/14

Y1 - 2023/12/14

N2 - 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.

AB - 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.

U2 - 10.33011/livecoms.5.1.2375

DO - 10.33011/livecoms.5.1.2375

M3 - Article

SN - 2575-6524

VL - 5

JO - Living Journal of Computational Molecular Science

JF - Living Journal of Computational Molecular Science

IS - 1

ER -

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

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Projects

EPSRC Flagship Software - BioSimSpace A shared space for the community development of biomolecular simulation workflows

Cite this