Skip to content

Commit 8593aaf

Browse files
simongravellesimongravelle
committed
improved before your start
1 parent 9e63d86 commit 8593aaf

File tree

3 files changed

+83
-92
lines changed

3 files changed

+83
-92
lines changed

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

Lines changed: 3 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,4 @@
1-
You can access all the input scripts and data files that
2-
are used in these tutorials from |Github_repository|.
3-
4-
.. |Github_repository| raw:: html
1+
.. include:: links.rst
52

6-
<a href="https://github.com/gromacstutorials/gromacstutorials-inputs" target="_blank">GitHub</a>
3+
You can access all the input scripts and data files that
4+
are used in these tutorials from |GitHub-repository|.

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

Lines changed: 41 additions & 87 deletions
Original file line numberDiff line numberDiff line change
@@ -1,97 +1,52 @@
11
.. _contact-before-you-start-label:
2+
.. include:: links.rst
23

3-
Before you start
4+
Before You Start
45
****************
56

6-
.. container:: justify
7+
The GROMACS tutorials in this series are organized by increasing complexity. If
8+
you're completely new to GROMACS, it's strongly recommended to begin with the
9+
first tutorial on a simple :ref:`bulk-solution-label` to get familiar with the
10+
software and workflow.
711

8-
*GROMACS tutorials* is made of several tutorials that are
9-
ordered by increasing difficulty.
10-
11-
Required software
12+
Required Software
1213
=================
1314

14-
.. container:: justify
15-
16-
The 2024.2 version of GROMACS is required
17-
to follow the tutorials.
18-
19-
GROMACS (2024.2)
20-
----------------
21-
22-
.. container:: justify
23-
24-
Download and install the 2024.2 version of GROMACS by following the
25-
instructions of the |gromacs-manual|.
26-
Depending on your operative system (i.e. Linux, macOS, or Windows),
27-
the procedure may differ.
28-
29-
.. |gromacs-manual| raw:: html
30-
31-
<a href="https://manual.gromacs.org/current/index.html" target="_blank">GROMACS manual</a>
15+
Each tutorial specifies the minimum required version of GROMACS at the top.
16+
While most examples should work with any recent version, using a different
17+
version may lead to unexpected errors or differences in behavior or output.
18+
When possible, try to match the GROMACS version used in the
19+
tutorial when possible.
3220

33-
VMD (optional)
34-
--------------
21+
GROMACS
22+
-------
3523

36-
.. container:: justify
24+
Download and install GROMACS by following the instructions in the
25+
|gromacs-manual|. The installation procedure may vary depending on your
26+
operating system (e.g., Linux, macOS, or Windows).
3727

38-
In order to visualize the simulation, the version
39-
1.9.3 of |VMD| will be used :cite:`humphreyVMDVisualMolecular1996`.
40-
Some basic instructions for VMD are given on *lammpstutorials*, see
41-
|VMD-lammps-tutorials|. If you prefer, feel free to use an alternative visualization
42-
software like |Ovito|.
28+
VMD
29+
---
4330

44-
.. |VMD-lammps-tutorials| raw:: html
45-
46-
<a href="https://lammpstutorials.github.io/sphinx/build/html/tutorials/vmd/vmd-tutorial.html" target="_blank">this link</a>
47-
48-
.. |VMD| raw:: html
49-
50-
<a href="https://www.ks.uiuc.edu/Research/vmd" target="_blank">VMD</a>
51-
52-
.. |Ovito| raw:: html
53-
54-
<a href="https://www.ovito.org" target="_blank">Ovito</a>
31+
In order to visualize the simulation, install Visual Molecular Dynamics (|VMD|)
32+
:cite:`humphreyVMDVisualMolecular1996`. Version 1.9.3 of VMD was used to
33+
create the images in this website, but more recent versions should work as
34+
well. If you prefer, feel free to use an alternative visualization software.
5535

5636
Python (optional)
5737
-----------------
5838

59-
.. container:: justify
60-
61-
The version 2.6.1 of MDAnalysis is used
62-
together with the version 3.11.4
63-
of Python :cite:`vanrossumPythonTutorial1995, michaud-agrawalMDAnalysisToolkitAnalysis2011`.
64-
65-
.. container:: justify
66-
67-
To plot the results from the simulations,
68-
the version 3.5.2 of |Matplotlib Pyplot| is used.
69-
70-
.. |Matplotlib Pyplot| raw:: html
71-
72-
<a href="https://matplotlib.org/3.5.3/api/_as_gen/matplotlib.pyplot.html" target="_blank">Matplotlib Pyplot</a>
39+
The version 2.6.1 of MDAnalysis is used together with version 3.11.4 of
40+
Python :cite:`vanrossumPythonTutorial1995,michaud-agrawalMDAnalysisToolkitAnalysis2011`.
41+
To plot the results from the simulations, version 3.5.2 of |Matplotlib-Pyplot| is used.
42+
All the script used to generate the plots are available from |GitHub-repository|.
7343

7444
Text editing software
7545
---------------------
7646

77-
.. container:: justify
78-
79-
To write and edit GROMACS input files, a text editor is required.
80-
Any text editor will do, such as |gedit|,
81-
|vim|,
82-
or |vscode|.
83-
84-
.. |gedit| raw:: html
85-
86-
<a href="https://help.gnome.org/users/gedit/stable/" target="_blank">gedit</a>
87-
88-
.. |vim| raw:: html
89-
90-
<a href="https://www.vim.org/" target="_blank">vim</a>
91-
92-
.. |vscode| raw:: html
93-
94-
<a href="https://code.visualstudio.com/" target="_blank">vscode</a>
47+
To write and edit GROMACS input files, a text editor is required.
48+
Any plain text editor will do, such as |gedit|, |vim|, or |vscode|,
49+
|nano|, |sublime|, and |notepadpp|.
9550

9651
Find the input scripts
9752
======================
@@ -101,15 +56,14 @@ Find the input scripts
10156
Recommended reading
10257
===================
10358

104-
.. container:: justify
105-
106-
To better understand molecular dynamics simulations, I recommend the reading
107-
of *Understanding molecular simulation* by Daan Frenkel and Berend
108-
Smit :cite:`frenkelUnderstandingMolecularSimulation2002`, as well as
109-
*Computer simulation of liquids* by Michael Allen and Dominic Tildesley
110-
:cite:`allenComputerSimulationLiquids2017`. To understand the basic concepts
111-
of fluid and Soft Matter systems, I recommend reading *Basic concepts for
112-
simple and complex liquids* by Jean-Louis Barrat and Jean-Pierre Hansen
113-
:cite:`barratBasicConceptsSimple2003`,
114-
as well as *Theory of simple liquids: with applications to soft matter*
115-
by Jean-Pierre Hansen and Ian Ranald McDonald :cite:`hansenTheorySimpleLiquids2013a`.
59+
To better understand molecular dynamics simulations, I recommend the reading of
60+
*Understanding Molecular Simulation* by Daan Frenkel and Berend Smit
61+
:cite:`frenkelUnderstandingMolecularSimulation2002`, as well as *Computer
62+
Simulation of Liquids* by Michael Allen and Dominic Tildesley
63+
:cite:`allenComputerSimulationLiquids2017`.
64+
65+
To understand the basic concepts of fluid and Soft Matter systems, I recommend
66+
reading *Basic Concepts for Simple and Complex Liquids* by Jean-Louis Barrat and
67+
Jean-Pierre Hansen :cite:`barratBasicConceptsSimple2003`, as well as *Theory of
68+
Simple Liquids: With Applications to Soft Matter* by Jean-Pierre Hansen and Ian
69+
Ranald McDonald :cite:`hansenTheorySimpleLiquids2013a`.

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

Lines changed: 39 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,39 @@
1+
.. |GitHub-repository| raw:: html
2+
3+
<a href="https://github.com/gromacstutorials/gromacstutorials-inputs" target="_blank">GitHub</a>
4+
5+
.. |Matplotlib-Pyplot| raw:: html
6+
7+
<a href="https://matplotlib.org/3.5.3/api/_as_gen/matplotlib.pyplot.html" target="_blank">Matplotlib Pyplot</a>
8+
9+
.. |gromacs-manual| raw:: html
10+
11+
<a href="https://manual.gromacs.org/current/index.html" target="_blank">GROMACS manual</a>
12+
13+
.. |VMD| raw:: html
14+
15+
<a href="https://www.ks.uiuc.edu/Research/vmd" target="_blank">VMD</a>
16+
17+
.. |nano| raw:: html
18+
19+
<a href="https://www.nano-editor.org/" target="_blank">Nano</a>
20+
21+
.. |sublime| raw:: html
22+
23+
<a href="https://www.sublimetext.com/" target="_blank">Sublime Text</a>
24+
25+
.. |notepadpp| raw:: html
26+
27+
<a href="https://notepad-plus-plus.org/" target="_blank">Notepad++</a>
28+
29+
.. |gedit| raw:: html
30+
31+
<a href="https://help.gnome.org/users/gedit/stable/" target="_blank">Gedit</a>
32+
33+
.. |vim| raw:: html
34+
35+
<a href="https://www.vim.org/" target="_blank">Vim</a>
36+
37+
.. |vscode| raw:: html
38+
39+
<a href="https://code.visualstudio.com/" target="_blank">Visual Studio Code</a>

0 commit comments

Comments
 (0)