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FIX broken links (#436)
* close #405 * FIX broken links * add mamba instructions and refine installation quick start
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_posts/2024-05-27-gsoc-outreachy-students.md

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She will be documenting her internship journey on her [Medium blog](https://medium.com/@adetutuoluwasanmi). Feel free to check it out for updates on her experience!
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@BradyAJohnston @cbouy @hmacdope @IAlibay @jennaswa @micaela-matta @orbeckst @richardgowers @xhgchen @yuxuanzhuang (mentors and org admins)
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@BradyAJohnston @cbouy @hmacdope @IAlibay @jennaswa @micaela-matta @orbeckst @richardjgowers @xhgchen @yuxuanzhuang (mentors and org admins)
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[gsoc]: https://summerofcode.withgoogle.com
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[outreachy]: https://www.outreachy.org/

_posts/2024-08-30-gsoc2024-final-sm.md

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We also thank [Google](https://opensource.google/) for supporting the students and continuing to support MDAnalysis as a GSoC organization since 2016.
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@cbouy @hmacdope @IAlibay @jennaswa @richardgowers @xhgchen @yuxuanzhuang (mentors and org admins)
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@cbouy @hmacdope @IAlibay @jennaswa @richardjgowers @xhgchen @yuxuanzhuang (mentors and org admins)
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[blog-lawson]: {{ site.baseurl }}{% post_url 2024-08-03-gsoc2024_woods %}
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[blog-valerij]: {{ site.baseurl }}{% post_url 2024-08-02-gsoc2024_talagayev %}

_posts/2025-02-11-gsoc2024-final-lg.md

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Please note that in addition to code contributions, we highly value [participating in the MDAnalysis community](https://www.mdanalysis.org/#participating) in other ways, including submitting [general feedback](https://www.mdanalysis.org/about/#feedback) and [issues via the GitHub issue tracker](https://github.com/MDAnalysis/mdanalysis/issues) and/or engaging in discussions on the MDAnalysis [Discord server](https://discord.com/channels/807348386012987462/) (join using [this invite link](https://discord.com/invite/fXTSfDJyxE)) and [GitHub Discussions forum](https://github.com/MDAnalysis/mdanalysis/discussions).
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@cbouy @hmacdope @IAlibay @jennaswa @richardgowers @xhgchen @yuxuanzhuang (GSoC 2024 mentors and org admins)
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@cbouy @hmacdope @IAlibay @jennaswa @richardjgowers @xhgchen @yuxuanzhuang (GSoC 2024 mentors and org admins)
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[blog-luna]: {{ site.baseurl }}{% post_url 2025-02-09-Luna-Morrow-Final-Submission %}

about.md

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- **2024**: @ljwoods2, @lunamorrow, @talagayev
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- **2023**: @marinegor, @xhgchen
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- **2022**: @aya9aladdin, @BFedder
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- **2021**: @ojeda-e, @orioncohen
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- **2021**: @ojeda-e, @orionarcher
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- **2020**: @cbouy, @hmacdope, @yuxuanzhuang
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- **2019**: @NinadBhat
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- **2018**: @ayushsuhane, @davidercruz

index.md

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MDAnalysis allows one to read particle-based trajectories (including
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individual coordinate frames such as biomolecules in the PDB format)
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and access the atomic coordinates through
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[NumPy](https://numpy.scipy.org/) arrays. This provides a flexible and
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[NumPy](https://numpy.org/) arrays. This provides a flexible and
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relatively fast framework for complex analysis tasks. In addition,
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powerful atom
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[selection commands]({{site.pypi.docs}}/documentation_pages/selections.html)

pages/installation_quick_start.md

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order: 2
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---
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MDAnalysis offers two methods to install the released version. For most
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users we recommend the [*Conda*](#conda) installation method.
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MDAnalysis offers multiple installation methods. For most
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users we recommend [mamba][] installation method, a faster
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drop-in replacement for [conda][] .
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## Conda ##
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## Mamba ##
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If you don't have [conda][] installed yet, follow the [installation
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instructions for conda][].
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instructions for conda][]. Following that, install [mamba][] with:
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To install the lastest stable release with [conda][conda] do:
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{% highlight bash %}
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conda install -c conda-forge mamba
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{% endhighlight %}
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Then, install the latest stable release of MDAnalysis with:
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{% highlight bash %}
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conda config --add channels conda-forge
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conda install mdanalysis
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mamba install -c conda-forge mdanalysis
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{% endhighlight %}
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To upgrade to the latest stable release.
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To upgrade use:
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{% highlight bash %}
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conda update mdanalysis
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mamba update mdanalysis
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{% endhighlight %}
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To [run the test cases][run_tests] and examples, also install the unit tests (about 53 MiB
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To [run the test cases][run_tests] and examples, also install the unit tests (about 90 MB
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in size):
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{% highlight bash %}
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conda install MDAnalysisTests
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mamba install -c conda-forge MDAnalysisTests
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{% endhighlight %}
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The conda packages currently only support serial calculations. If you
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plan to use the parallel [OpenMP][OpenMP] algorithms you need to
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install MDAnalysis from the [Python Package
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Index](#python-package-index) and have a working OpenMP installation.
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MDAnalysis installed via mamba supports only serial calculations.
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If you need OpenMP-based parallelism, install MDAnalysis via [pip](#python-package-index)
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and ensure you have a working [OpenMP][] installation.
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## Python Package Index ##
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## More ##
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For more details on installation and alternative ways to install MDAnalysis see [Installing
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For more installation options and additional details see [Installing
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MDAnalysis in the {{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}/stable/installation.html).
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If you have questions with the installation, please ask on
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[{{site.mailinglists.discussion.name}}]({{site.mailinglists.discussion.url}}).
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[pip]: https://pip.pypa.io/en/latest/
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[mamba]:https://anaconda.org/conda-forge/mamba
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[conda]: https://conda.io/
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[installation instructions for conda]: https://conda.io/projects/conda/en/latest/user-guide/install/index.html
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[OpenMP]: https://www.openmp.org/

pages/learning_MDAnalysis.md

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@lilyminium's talk at [PyCon AU 2019](https://2019.pycon-au.org/) *The universe as balls and
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springs: molecular dynamics in Python* gives a general introduction to
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molecular dynamics and shows how to use MDAnalysis (and other tools
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such as [OpenMM](http://openmm.org/), [nglviewer](nglviewer.org/nglview/latest/),
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such as [OpenMM](http://openmm.org/), [nglviewer](https://nglviewer.org/nglview/latest/),
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[pandas](https://pandas.pydata.org/),
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[plotly](https://pandas.pydata.org/)). If you want to better
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pages/mdakits.md

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*If you have your own MDAKit and you would like to add it to the
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registry, please look at the [contribution instructions](https://mdakits.mdanalysis.org/add.html)
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registry, please look at the contribution [instructions](https://mdakits.mdanalysis.org/makingakit.html)
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or share it on [{{ site.mailinglists.discussion.name }}]({{ site.mailinglists.discussion.url }})!*
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