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<h1>Welcome to the GROMACS documentation!<a class="headerlink" href="#welcome-to-the-gromacs-documentation" title="Permalink to this headline">¶</a></h1>
<p>Contents:</p>
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<li class="toctree-l1"><a class="reference internal" href="download.html">Downloads</a><ul>
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<li class="toctree-l1"><a class="reference internal" href="release-notes/index.html">Release notes</a><ul>
<li class="toctree-l2"><a class="reference internal" href="release-notes/index.html#gromacs-2018-series">GROMACS 2018 series</a></li>
<li class="toctree-l2"><a class="reference internal" href="release-notes/index.html#gromacs-2016-series">GROMACS 2016 series</a></li>
<li class="toctree-l2"><a class="reference internal" href="release-notes/index.html#older-unmaintained-gromacs-series">Older (unmaintained) GROMACS series</a></li>
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<li class="toctree-l1"><a class="reference internal" href="install-guide/index.html">Installation guide</a><ul>
<li class="toctree-l2"><a class="reference internal" href="install-guide/index.html#introduction-to-building-gromacs">Introduction to building GROMACS</a></li>
<li class="toctree-l2"><a class="reference internal" href="install-guide/index.html#prerequisites">Prerequisites</a></li>
<li class="toctree-l2"><a class="reference internal" href="install-guide/index.html#doing-a-build-of-gromacs">Doing a build of GROMACS</a></li>
<li class="toctree-l2"><a class="reference internal" href="install-guide/index.html#special-instructions-for-some-platforms">Special instructions for some platforms</a></li>
<li class="toctree-l2"><a class="reference internal" href="install-guide/index.html#tested-platforms">Tested platforms</a></li>
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<li class="toctree-l1"><a class="reference internal" href="user-guide/index.html">User guide</a><ul>
<li class="toctree-l2"><a class="reference internal" href="user-guide/getting-started.html">Getting started</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/system-preparation.html">System preparation</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/managing-simulations.html">Managing long simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/faq.html">Answers to frequently asked questions (FAQs)</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/force-fields.html">Force fields in GROMACS</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/cutoff-schemes.html">Non-bonded cut-off schemes</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/cmdline.html">Command-line reference</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/mdp-options.html">Molecular dynamics parameters (.mdp options)</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/mdrun-features.html">Useful mdrun features</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/mdrun-performance.html">Getting good performance from <code class="docutils literal"><span class="pre">mdrun</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/run-time-errors.html">Common errors when using GROMACS</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/file-formats.html">File formats</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/terminology.html">Terminology</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/environment-variables.html">Environment Variables</a></li>
<li class="toctree-l2"><a class="reference internal" href="user-guide/floating-point.html">Floating point arithmetic</a></li>
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<ul class="simple">
<li><a class="reference external" href="manual-2018.1.pdf">Reference Manual</a> (PDF format)</li>
</ul>
<ul class="simple">
<li>Links to <a class="reference external" href="http://www.gromacs.org/Documentation/Tutorials">tutorial material</a></li>
</ul>
<div class="section" id="documentation-for-developers">
<h2>Documentation for developers<a class="headerlink" href="#documentation-for-developers" title="Permalink to this headline">¶</a></h2>
<p>The developer documentation currently consists of two parts:</p>
<ul class="simple">
<li>A developer guide that provides an overview of the GROMACS codebase, and
includes more detailed resouces such as guidelines and information on tools
used during development.</li>
<li>Doxygen documentation extracted from comments in C/C++ code, documenting the
actual C/C++ code.</li>
</ul>
<p>Some overview documentation that is closely related to the actual C/C++ code
appears in the Doxygen documentation, while some other overview content is in
the developer guide. The reasons are partially technical, but crosslinks
between the developer guide and the Doxygen documentation are provided whenever
related content appears split between the two sources.</p>
<p>The documentation does not yet cover all areas, but more content is being
(slowly) added.
Wiki pages at <<a class="reference external" href="http://www.gromacs.org/Developer_Zone">http://www.gromacs.org/Developer_Zone</a>> may contain additional
information (much of it outdated, though), and can be linked from relevant
locations in the developer guide.</p>
<p>Contents:</p>
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<ul>
<li class="toctree-l1"><a class="reference internal" href="dev-manual/index.html">Developer guide</a><ul>
<li class="toctree-l2"><a class="reference internal" href="dev-manual/overview.html">Codebase overview</a><ul>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/overview.html#source-code-organization">Source code organization</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/overview.html#documentation-organization">Documentation organization</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dev-manual/build-system.html">Build system overview</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="dev-manual/build-system.html#cmake-cache-variables">CMake cache variables</a></li>
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<li class="toctree-l3"><a class="reference internal" href="dev-manual/build-system.html#special-targets">Special targets</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/build-system.html#passing-information-to-source-code">Passing information to source code</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dev-manual/relocatable-binaries.html">Relocatable binaries</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="dev-manual/relocatable-binaries.html#finding-data-files">Finding data files</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/relocatable-binaries.html#known-issues">Known issues</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dev-manual/documentation-generation.html">Documentation generation</a><ul>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/documentation-generation.html#building-the-gromacs-documentation">Building the GROMACS documentation</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/documentation-generation.html#needed-build-tools">Needed build tools</a></li>
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<li class="toctree-l2"><a class="reference internal" href="dev-manual/style.html">Style guidelines</a><ul>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/formatting.html">Guidelines for code formatting</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/includestyle.html">Guidelines for #include directives</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/naming.html">Naming conventions</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/language-features.html">Allowed language features</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/doxygen.html">Using Doxygen</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/reportstyle.html">Guidelines for creating meaningful redmine issue reports</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/commitstyle.html">Guidelines for formatting of git commits</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/error-handling.html">Error handling</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="dev-manual/tools.html">Development-time tools</a><ul>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/doxygen.html">Using Doxygen</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/jenkins.html">Understanding Jenkins builds</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/releng/index.html">releng repository (missing)</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/gmxtree.html">Source tree checker scripts</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/uncrustify.html">Automatic source code formatting</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/testutils.html">Unit testing</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/tools.html#change-management">Change management</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/tools.html#build-system">Build system</a></li>
<li class="toctree-l3"><a class="reference internal" href="dev-manual/tools.html#code-formatting-and-style">Code formatting and style</a></li>
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</li>
</ul>
</li>
</ul>
</div>
<ul class="simple">
<li>Doxygen documentation<ul>
<li><dl class="first docutils">
<dt><a class="reference external" href="doxygen/html-user/index.xhtml">Public API documentation</a></dt>
<dd>This contains documentation for code that appears in installed headers,
as well as some overview documentation to understand those parts of the
code.
Please note that the definition of the public API is very preliminary
and subject to change, in particular for parts that have not been
documented.</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt><a class="reference external" href="doxygen/html-lib/index.xhtml">Code documentation</a></dt>
<dd>This contains the public API documentation as a subset, but also has more
details on the internal implementation of GROMACS. This is a good
place to start to understand some specific area of the code in general
to, e.g., contribute.</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt><a class="reference external" href="doxygen/html-full/index.xhtml">Full documentation</a></dt>
<dd>This contains every single documented function from the codebase,
including internal There can be an overwhelming amount of detail, but
this can be useful if trying to find some specific function within the
codebase.</dd>
</dl>
</li>
</ul>
</li>
</ul>
</div>
</div>
<div class="section" id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
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<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
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<li><a class="reference internal" href="#">Welcome to the GROMACS documentation!</a><ul>
<li><a class="reference internal" href="#documentation-for-developers">Documentation for developers</a></li>
</ul>
</li>
<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
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