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Merge pull request #24 from gromacstutorials/improve-annexes
Improve annexes
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‎docs/sphinx/source/non-tutorials/accessfile.rst‎

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You can access all the input scripts and data files that
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are used in these tutorials from |Github_repository|.
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.. |Github_repository| raw:: html
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.. include:: links.rst
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<a href="https://github.com/gromacstutorials/gromacstutorials-inputs" target="_blank">GitHub</a>
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You can access all the input scripts and data files that
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are used in these tutorials from |GitHub-repository|.

‎docs/sphinx/source/non-tutorials/before-you-start.rst‎

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.. _contact-before-you-start-label:
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.. include:: links.rst
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Before you start
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Before You Start
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****************
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.. container:: justify
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The GROMACS tutorials in this series are organized by increasing complexity. If
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you're completely new to GROMACS, it's strongly recommended to begin with the
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first tutorial on a simple :ref:`bulk-solution-label` to get familiar with the
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software and workflow.
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*GROMACS tutorials* is made of several tutorials that are
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ordered by increasing difficulty.
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Required software
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Required Software
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=================
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.. container:: justify
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The 2024.2 version of GROMACS is required
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to follow the tutorials.
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GROMACS (2024.2)
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----------------
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.. container:: justify
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Download and install the 2024.2 version of GROMACS by following the
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instructions of the |gromacs-manual|.
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Depending on your operative system (i.e. Linux, macOS, or Windows),
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the procedure may differ.
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.. |gromacs-manual| raw:: html
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<a href="https://manual.gromacs.org/current/index.html" target="_blank">GROMACS manual</a>
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Each tutorial specifies the minimum required version of GROMACS at the top.
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While most examples should work with any recent version, using a different
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version may lead to unexpected errors or differences in behavior or output.
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When possible, try to match the GROMACS version used in the
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tutorial when possible.
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VMD (optional)
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--------------
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GROMACS
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-------
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.. container:: justify
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Download and install GROMACS by following the instructions in the
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|gromacs-manual|. The installation procedure may vary depending on your
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operating system (e.g., Linux, macOS, or Windows).
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In order to visualize the simulation, the version
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1.9.3 of |VMD| will be used :cite:`humphreyVMDVisualMolecular1996`.
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Some basic instructions for VMD are given on *lammpstutorials*, see
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|VMD-lammps-tutorials|. If you prefer, feel free to use an alternative visualization
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software like |Ovito|.
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VMD
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---
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.. |VMD-lammps-tutorials| raw:: html
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<a href="https://lammpstutorials.github.io/sphinx/build/html/tutorials/vmd/vmd-tutorial.html" target="_blank">this link</a>
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.. |VMD| raw:: html
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<a href="https://www.ks.uiuc.edu/Research/vmd" target="_blank">VMD</a>
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.. |Ovito| raw:: html
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<a href="https://www.ovito.org" target="_blank">Ovito</a>
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In order to visualize the simulation, install Visual Molecular Dynamics (|VMD|)
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:cite:`humphreyVMDVisualMolecular1996`. Version 1.9.3 of VMD was used to
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create the images in this website, but more recent versions should work as
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well. If you prefer, feel free to use an alternative visualization software.
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Python (optional)
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-----------------
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.. container:: justify
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The version 2.6.1 of MDAnalysis is used
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together with the version 3.11.4
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of Python :cite:`vanrossumPythonTutorial1995, michaud-agrawalMDAnalysisToolkitAnalysis2011`.
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.. container:: justify
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To plot the results from the simulations,
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the version 3.5.2 of |Matplotlib Pyplot| is used.
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.. |Matplotlib Pyplot| raw:: html
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<a href="https://matplotlib.org/3.5.3/api/_as_gen/matplotlib.pyplot.html" target="_blank">Matplotlib Pyplot</a>
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The version 2.6.1 of MDAnalysis is used together with version 3.11.4 of
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Python :cite:`vanrossumPythonTutorial1995,michaud-agrawalMDAnalysisToolkitAnalysis2011`.
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To plot the results from the simulations, version 3.5.2 of |Matplotlib-Pyplot| is used.
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All the script used to generate the plots are available from |GitHub-repository|.
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Text editing software
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---------------------
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.. container:: justify
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To write and edit GROMACS input files, a text editor is required.
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Any text editor will do, such as |gedit|,
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|vim|,
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or |vscode|.
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.. |gedit| raw:: html
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<a href="https://help.gnome.org/users/gedit/stable/" target="_blank">gedit</a>
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.. |vim| raw:: html
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<a href="https://www.vim.org/" target="_blank">vim</a>
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.. |vscode| raw:: html
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<a href="https://code.visualstudio.com/" target="_blank">vscode</a>
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To write and edit GROMACS input files, a text editor is required.
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Any plain text editor will do, such as |gedit|, |vim|, or |vscode|,
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|nano|, |sublime|, and |notepadpp|.
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Find the input scripts
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======================
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Recommended reading
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===================
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To better understand molecular dynamics simulations, I recommend the reading
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of *Understanding molecular simulation* by Daan Frenkel and Berend
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Smit :cite:`frenkelUnderstandingMolecularSimulation2002`, as well as
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*Computer simulation of liquids* by Michael Allen and Dominic Tildesley
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:cite:`allenComputerSimulationLiquids2017`. To understand the basic concepts
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of fluid and Soft Matter systems, I recommend reading *Basic concepts for
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simple and complex liquids* by Jean-Louis Barrat and Jean-Pierre Hansen
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:cite:`barratBasicConceptsSimple2003`,
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as well as *Theory of simple liquids: with applications to soft matter*
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by Jean-Pierre Hansen and Ian Ranald McDonald :cite:`hansenTheorySimpleLiquids2013a`.
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To better understand molecular dynamics simulations, I recommend the reading of
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*Understanding Molecular Simulation* by Daan Frenkel and Berend Smit
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:cite:`frenkelUnderstandingMolecularSimulation2002`, as well as *Computer
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Simulation of Liquids* by Michael Allen and Dominic Tildesley
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:cite:`allenComputerSimulationLiquids2017`.
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To understand the basic concepts of fluid and Soft Matter systems, I recommend
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reading *Basic Concepts for Simple and Complex Liquids* by Jean-Louis Barrat and
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Jean-Pierre Hansen :cite:`barratBasicConceptsSimple2003`, as well as *Theory of
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Simple Liquids: With Applications to Soft Matter* by Jean-Pierre Hansen and Ian
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Ranald McDonald :cite:`hansenTheorySimpleLiquids2013a`.

‎docs/sphinx/source/non-tutorials/contact.rst‎

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.. _contact-label:
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.. include:: links.rst
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Contact us
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**********
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About
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*****
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Struggling with your simulation project?
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========================================
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.. figure:: figures/patreon.png
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:height: 100
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:alt: Simon gravelle patreon for LAMMPS and GROMACS material
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:align: right
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:target: https://www.patreon.com/molecularsimulations
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Connect with experts and get your questions answered directly in our
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|patreon-discord| Discord channel.
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.. |patreon-discord| raw:: html
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Since its launch, this website has evolved considerably—and will
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likely continue to do so. Suggestions are always welcome.
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<a href="https://www.patreon.com/molecularsimulations" target="_blank">"Molecular Simulations"</a>
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Contact me by email
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===================
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Feel free to reach out to me with suggestions, to report issues with the
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website, or to ask general questions about GROMACS or molecular simulations.
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My email address is available on my |personal-page|.
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Support the GROMACS tutorials initiative
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Struggling with your simulation project?
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========================================
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You can support this webpage through |patreon|. As a supporter,
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you will receive personalized support and assistance with your projects.
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.. |patreon| raw:: html
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<a href="https://www.patreon.com/molecularsimulations" target="_blank">Patreon</a>
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Follow us
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=========
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.. container:: justify
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- |github_gromacs_tutorials| community account
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- |twitter_gromacs_tutorials| community account
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- Creator's |personal_page_simon_gravelle|
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- |twitter_simon_gravelle| personal account
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- |github_simon_gravelle| personal account
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.. |github_gromacs_tutorials| raw:: html
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<a href="https://github.com/gromacstutorials" target="_blank">GitHub</a>
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.. |twitter_gromacs_tutorials| raw:: html
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<a href="https://x.com/gmxtutorials" target="_blank">Twitter</a>
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.. |personal_page_simon_gravelle| raw:: html
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<a href="https://simongravelle.github.io/" target="_blank">personal page</a>
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.. |twitter_simon_gravelle| raw:: html
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<a href="https://twitter.com/GravelleSimon" target="_blank">Twitter</a>
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.. |github_simon_gravelle| raw:: html
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<a href="https://github.com/simongravelle" target="_blank">GitHub</a>
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You can register on |patreon| to receive personalized help with your research
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project, or simply to support the continued development of this project.

‎docs/sphinx/source/non-tutorials/figures/patreon.png‎

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