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‎docs/doc-sphinx/source/index.rst

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@@ -10,7 +10,7 @@ Welcome to gromacstutorials's documentation!
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:maxdepth: 2
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:caption: Main
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howto.rst
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non-tutorials/before-you-start.rst
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contact/contact.rst
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.. toctree::

‎docs/doc-sphinx/source/non-tutorials/accessfile.rst

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.. container:: justify
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You can access the input scripts and data files that
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are used in these tutorials from |Github_repository_input_folder|.
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.. |Github_repository_input_folder| raw:: html
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<a href="https://github.com/gromacstutorials" target="_blank">this Github repository</a>

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

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.. _contact-before-you-start-label:
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Before you start
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****************
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.. container:: justify
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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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=================
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.. container:: justify
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The 2023.3 version of GROMACS is required
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to follow the tutorials.
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GROMACS (2023.3)
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----------------
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.. container:: justify
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Download and install the 2023.3 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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VMD (optional)
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--------------
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.. container:: justify
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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:`humphrey1996vmd`.
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Some basic instructions for VMD are given here in the
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:ref:`vmd-label`. If you prefer, feel free to use an alternative visualization
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software like |Ovito|.
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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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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:`van1995python, michaud2011mdanalysis, gowers2016mdanalysis`.
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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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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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Find the input scripts
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======================
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.. include:: ../non-tutorials/accessfile.rst
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Recommended reading
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===================
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.. container:: justify
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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:`frenkel2023understanding`, as well as
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*Computer simulation of liquids* by Michael Allen and Dominic Tildesley
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:cite:`allen2017computer`. 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:`barrat2003basic`,
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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:`hansen2013theory`.

‎docs/doc-sphinx/source/tutorials/bulksolution.rst

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.. container:: hatnote
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The very basics of GROMACS through a
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simple example
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The very basics of GROMACS through a simple example
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.. figure:: figures/bulksolution/video-solution-light.webp
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:alt: Water solution of SO\ :sub:`4`\ :sup:`2-` and Na\ :sup:`+` ions visualized with VMD
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with sodium (Na\ :sup:`+`) and sulfate
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(SO\ :sub:`4`\ :sup:`2-`) ions.
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.. container:: justify
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This tutorial illustrates several major ingredients of molecular
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dynamics simulations, such as energy minimization,
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thermostating, NVT and NPT equilibration, and
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trajectory visualisation.
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There are no prerequisite to follow this tutorial.
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.. include:: ../contact/needhelp.rst
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Required softwares
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==================
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.. container:: justify
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GROMACS must be installed on your machine. You can
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install it following the instructions of the |gromacs-manual|.
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Alternatively, if you are using Ubuntu OS, you can
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simply execute the following command in a terminal:
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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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.. code-block:: bw
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sudo apt-get install gromacs
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.. container:: justify
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You can verify that GROMACS is indeed installed on your
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computer by typing in a terminal :
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.. code-block:: bw
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gmx
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.. container:: justify
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You should see the version of GROMACS that has been
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installed. On my computer I see
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.. code-block:: bw
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:-) GROMACS - gmx, 2023 (-:
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Executable: /usr/bin/gmx
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Data prefix: /usr
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(...)
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.. container:: justify
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as well as a quote (at the bottom), such as
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.. code-block:: bw
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(...)
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GROMACS reminds you: "Computers are like humans - they do everything except think." (John von Neumann)
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.. container:: justify
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In addition to GROMACS, you will also need
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- |(1) a basic text editing software| such as Vim, Gedit, or Notepad++,
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- |(2) a visualization software|, here I will use VMD (note: VMD is free but you have to register to the uiuc website in order to download it. If you don't want to, you can also use Ovito.),
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- |(3) a plotting tool| like XmGrace or pyplot.
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.. |LAMMPS website| raw:: html
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<a href="https://lammps.sandia.gov" target="_blank">LAMMPS website</a>
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.. |(1) a basic text editing software| raw:: html
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<a href="https://help.gnome.org/users/gedit/stable/" target="_blank">(1) a basic text editing software</a>
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.. |(2) a visualization software| raw:: html
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<a href="https://www.ks.uiuc.edu/Research/vmd/" target="_blank">(2) a visualization software</a>
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.. |(3) a plotting tool| raw:: html
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<a href="https://plasma-gate.weizmann.ac.il/Grace/" target="_blank">(3) a plotting tool</a>
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The input files
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===============
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In order to run the present simulation using GROMACS,
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we need the 3 following files (or sets of files):
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- 1) a **configuration file** (.gro) containing the
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- 1) A **configuration file** (.gro) containing the
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initial positions of the atoms and the box
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dimensions,
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- 2) a **topology file** (.top) specifying the
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location of the force field files (.itp),
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- 3) an **input file** (.mdp) containing the
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dimensions.
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- 2) A **topology file** (.top) specifying the
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location of the force field files (.itp).
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- 3) An **input file** (.mdp) containing the
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parameters of the simulation (e.g. temperature, timestep).
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1) The configuration file (.gro)
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--------------------------------
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