.. _contact-before-you-start-label:
Before you start
****************
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*GROMACS tutorials* is made of several tutorials that are
ordered by increasing difficulty.
Required software
=================
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The 2024.2 version of GROMACS is required
to follow the tutorials.
GROMACS (2024.2)
----------------
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Download and install the 2024.2 version of GROMACS by following the
instructions of the |gromacs-manual|.
Depending on your operative system (i.e. Linux, macOS, or Windows),
the procedure may differ.
.. |gromacs-manual| raw:: html
GROMACS manual
VMD (optional)
--------------
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In order to visualize the simulation, the version
1.9.3 of |VMD| will be used :cite:`humphrey1996vmd`.
Some basic instructions for VMD are given on *lammpstutorials*, see
|VMD-lammps-tutorials|. If you prefer, feel free to use an alternative visualization
software like |Ovito|.
.. |VMD-lammps-tutorials| raw:: html
this link
.. |VMD| raw:: html
VMD
.. |Ovito| raw:: html
Ovito
Python (optional)
-----------------
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The version 2.6.1 of MDAnalysis is used
together with the version 3.11.4
of Python :cite:`van1995python, michaud2011mdanalysis, gowers2016mdanalysis`.
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To plot the results from the simulations,
the version 3.5.2 of |Matplotlib Pyplot| is used.
.. |Matplotlib Pyplot| raw:: html
Matplotlib Pyplot
Text editing software
---------------------
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To write and edit GROMACS input files, a text editor is required.
Any text editor will do, such as |gedit|,
|vim|,
or |vscode|.
.. |gedit| raw:: html
gedit
.. |vim| raw:: html
vim
.. |vscode| raw:: html
vscode
Find the input scripts
======================
.. include:: ../non-tutorials/accessfile.rst
Recommended reading
===================
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To better understand molecular dynamics simulations, I recommend the reading
of *Understanding molecular simulation* by Daan Frenkel and Berend
Smit :cite:`frenkel2023understanding`, as well as
*Computer simulation of liquids* by Michael Allen and Dominic Tildesley
:cite:`allen2017computer`. To understand the basic concepts
of fluid and Soft Matter systems, I recommend reading *Basic concepts for
simple and complex liquids* by Jean-Louis Barrat and Jean-Pierre Hansen
:cite:`barrat2003basic`,
as well as *Theory of simple liquids: with applications to soft matter*
by Jean-Pierre Hansen and Ian Ranald McDonald :cite:`hansen2013theory`.