Jupyter Notebook Protein MD Setup tutorial
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Download RO CrateProtein MD Setup tutorial 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). The particular example used is the Lysozyme protein (PDB code 1AKI).
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 2 (latest) Created 1st Jul 2021 at 15:51 by Douglas Lowe
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Version 1 (earliest) Created 7th May 2021 at 14:51 by Douglas Lowe
Uses GROMACS 2020.4 and BioExcel Building Blocks version 3.5. Taken from Git commit a81b483
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Creators and SubmitterViews: 1720 Downloads: 9
Created: 7th May 2021 at 14:51
Last updated: 17th Mar 2022 at 09:01
Last used: 11th Aug 2022 at 12:10
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Teams: BioBB Building Blocks
Organizations: The University of Manchester
https://orcid.org/0000-0002-1248-3594
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.
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Public web page: https://mmb.irbbarcelona.org/biobb/
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Number of items: 5
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Selection of BioExcel Building Blocks (BioBB) Workflows intended for tutorials and training.
