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<!DOCTYPE html>
<html>
<head>
<meta charset='utf-8'>
<title>Collective variables library</title>
<meta name="description" content="Home Page of the Collective Variables Library, or Colvars">
<meta name="keywords" content="colvars, collective variables, reaction coordinate, GROMACS, LAMMPS, NAMD, Tinker-HP, VMD, free-energy, potential of mean force, molecular dynamics, ABF, metadynamics, umbrella sampling, WHAM">
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<body>
<div id="container">
<div class="inner">
<header>
<h1>Colvars</h1>
<h2>Collective variables library for molecular simulation and analysis programs </h2>
</header>
<section id="downloads" class="clearfix">
<a href="https://github.com/Colvars/colvars/archive/master.zip" id="download-zip" class="button"><span>Download .zip</span></a>
<a href="https://github.com/Colvars/colvars/archive/master.tar.gz" id="download-tar-gz" class="button"><span>Download .tar.gz</span></a>
<a href="https://github.com/Colvars/colvars" id="view-on-github" class="button"><span>View on GitHub</span></a>
</section>
<hr>
<section id="main_content">
<p>A software library for molecular simulation programs, which provides a flexible and high-performance platform for present and future algorithms (<a href="http://www.tandfonline.com/doi/abs/10.1080/00268976.2013.813594">reference article</a>).</p>
<h3>Reference manual:</h3>
<ul>
<li>LAMMPS version: <a href="master/colvars-refman-lammps.pdf" id="download-lammps">PDF</a> <a href="master/colvars-refman-lammps.html">HTML</a></li>
<li>NAMD version: <a href="master/colvars-refman-namd.pdf">PDF</a> <a href="master/colvars-refman-namd.html">HTML</a></li>
<li>GROMACS version: <a href="master/colvars-refman-gromacs.pdf">PDF</a> <a href="master/colvars-refman-gromacs.html">HTML</a></li>
<li>Tinker-HP version: <a href="master/colvars-refman-tinkerhp.pdf">PDF</a> <a href="master/colvars-refman-tinkerhp.html">HTML</a></li>
<li>VMD version: <a href="master/colvars-refman-vmd.pdf">PDF</a> <a href="master/colvars-refman-vmd.html">HTML</a></li>
</ul>
<div id="examples">
<h3>Example configurations:</h3>
</div>
<ul>
<li>Check the examples repository <a href="https://github.com/Colvars/examples">https://github.com/Colvars/examples</a>, and particularly the detailed <a href="https://github.com/Colvars/examples/blob/master/15leu2x/Instructions.pdf?raw=true">instruction set</a>.</li>
<li>Check also the <a href="https://github.com/Colvars/colvars/blob/master/examples?raw=true">examples</a> folder inside the code repository: examples include configuration files for <a href="https://github.com/Colvars/colvars/blob/master/examples/01_NOE_restraints.colvars.in?raw=true">NMR restraints</a>, <a href="https://github.com/Colvars/colvars/blob/master/examples/05_targeted_MD.colvars.in?raw=true">targeted MD</a>, and to define the <a href="https://github.com/Colvars/colvars/blob/master/examples/08_relative_rotation.colvars.in?raw=true">relative orientation</a> of two flexible objects.</li>
</ul>
<h3>To use the latest version of this code:</h3>
<ul>
<li>Check the <a href="https://lammps.sandia.gov/download.html">LAMMPS precompiled binaries</a>, the <a href="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD">nightly builds of NAMD</a>, or <a href="https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD">the alpha versions of VMD</a>.</li>
OR
<li>Download this repository and run the update-colvars-code.sh script to update the source code of the program of your choice. This approach is normally useful on ly for VMD, where the source code updates are infrequent.</li>
</ul>
<h3>To report bugs or to suggest new features:</h3>
<p>Use the <a href="https://github.com/Colvars/colvars/issues">Issues</a> tab of our Github page.</p>
<h3>To extend the code</h3>
<p>A working implementation of a new variable or a new algorithm can be
achieved already with <b>scripted functions</b>, without changes to the
C++ code: see the reference manuals for details. Depending on how much
the scripted code reuses binary code, this may be already efficient, or
require changes to the underlying code.</p>
<p> For further flexibility and optimization, it is possible to modify the C++
code: details are available through the
C++ <a href="doxygen/html/index.html">class documentation</a>. One
notable example is <b>adding a new type of collective variable</b>, which
is described <a href="doxygen/html/classcolvar_1_1cvc.html#details">here</a>.</p>
<h3>License</h3>
<p>This software is distributed under the GNU Lesser General Public License,
version 3.</p>
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