Jupyter Notebook ABC MD Setup tutorial
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Download RO-CrateAMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)
Based on the official GROMACS tutorial.
This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).
- (c) 2015-2022 Barcelona Supercomputing Center
- (c) 2015-2022 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Version History
Version 6 (latest) Created 6th Aug 2025 at 14:38 by Genís Bayarri
Update to 5.1.*
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Version-65bbbdf6
Version 4 Created 26th Jul 2023 at 10:39 by Genís Bayarri
Fixed importlib_metadata bug
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Version-4
e91b3bc
Version 3 Created 14th Apr 2023 at 09:42 by Genís Bayarri
Update to BioBB 4.0.*
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Version-3
a4388d0
Version 2 Created 23rd Nov 2022 at 08:57 by Genís Bayarri
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version-2
2ccc69e
Version 2 (earliest) Created 28th Sep 2021 at 14:24 by Genís Bayarri
Updated to biobb 3.8.*. Taken from Git commit e3f4d687bed26bf2f247df8e4d064f44ff1fd280
Frozen
Version-2
e3f4d68
Creators and Submitter
Views: 7486 Downloads: 2689
Created: 28th Sep 2021 at 14:24
Last updated: 6th Aug 2025 at 14:40
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https://orcid.org/0000-0003-0513-0288
BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. Established in 2015, the centre has grown into a major research and innovation hub for scientific computing. BioExcel develops some of the most popular applications for modelling and simulations of biomolecular systems. A broad range of additional pre-/post-processing tools are integrated with the core applications within user-friendly workflows and container solutions.
The software stack comes with ...
Teams: BioBB Building Blocks, BioExcel Best Practice Guides
Web page: https://bioexcel.eu/
The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...
Space: BioExcel
Public web page: https://mmb.irbbarcelona.org/biobb/
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work ...
