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<!doctype html>
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<head>
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<meta name="description" content="Q molecular dynamics">
<title>Q for Molecular Dynamics – </title>
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<a class="pure-menu-heading" href="">Q</a>
<ul>
<li><a href="#introduction">Introduction</a></li>
<li><a href="#documentation">Documentation</a></li>
<li><a href="examples/examples.html">Examples</a></li>
<li><a href="ff/forcefields.html">Force Fields</a></li>
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<li><a href="#support">Support</a></li>
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<h1>Q - Our Molecular Dynamics Program</h1>
</div>
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<img class="pure-img-responsive" src="img/qlogo_200.png"
alt="Q logo">
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<h2>Free energy calculations in biomolecular systems</h2>
</div>
<div class="content">
<h2 class="content-subhead"><span id="introduction">Introduction</span></h2>
<p>Molecular dynamics (MD) simulation can be used to
sample the thermally accessible region of conformational space of a
microscopic model of a molecular system. From the ensemble of sampled
structures and their associated potential energies (given by the force
field or molecular mechanics potential energy function) it is, in
principle, possible to calculate free energies. Quantities such as
binding free energies, solvation free energies and activation free
energies are particularly interesting to calculate because they are
the direct result of thermodynamic or kinetic experiments. It is thus
possible both to quantitatively verify calculated results against
experimental data and to make predictions which can be tested
experimentally. Q is a set of tools for such calculations, tailored
for some specific kinds of free energy calculations, namely:
<ul>
<li>(I) Free energy perturbation (FEP) simulations.</li>
<li>(II) Empirical valence bond (EVB) calculations of reaction free energies.</li>
<li>(III) Linear interaction energy (LIE) calculations of receptor-ligand binding
affinities.
</li>
</ul>
</p>
<h2 class="content-subhead"><span id="documentation">Documentation</span></h2>
<p>The Q manual is only available on-line as a PDF file.</p>
<ul>
<li><a href="documents/qman.pdf">Q version 5 manual in PDF format</a></li>
</ul>
The latest changes are briefly documented in the version
history files:
<ul>
<li><a href="history/qdyn_history.txt">qdyn version history</a></li>
<li><a href="history/qprep_history.txt">qprep version history</a></li>
<li><a href="history/qcalc_history.txt">qcalc version history</a></li>
<li><a href="history/qfep_history.txt">qfep version history</a></li>
</ul>
<h2 class="content-subhead"><span id="evaluation">Evaluation Version</span></h2>
<p>If you want to try Q before requesting a license, we provide an
evaluation kit. The kit contains executable images for the Q programs
for the Win32/Intel x86 platform (i.e. Windows95, Windows98, WindowsNT
running on Pentium-like processors). The evaluation programs were
built with all compiler optimizations disabled and therefore run at
less than 20% of the speed of the optimized programs. Only Gromos87
force field files are included in the kit.</p>
<ul>
<li><a href="">Download evaluation kit for windows.</a></li>
<li><a href="">Download evaluation kit for linux.</a></li>
</ul>
<p>To get started in setting up your own test simulations, you
probably want to look at the Q examples available on-line.</p>
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<h2 class="content-subhead">Obtaining the program</h2>
<p> You can get Q from the following link:</p>
<a href="https://github.com/esguerra/Q6">https://github.com/esguerra/Q6</a>
<p>Q is now under a GPL Version 2 License. This means that you can copy the code and modify it at will, but if you make any changes you should give them back
to the copyright holders.</p>
<!--
<p>License to use Q is offered by the company Uppsala Molekylmekaniska
HB which is owned by the Q developers.</p>
<h2 class="content-subhead"><span id="license">For non-commercial use</span></h2>
<p>Our policy is to distribute the program, complete with source code,
without charge to academic institutions and to other non-profit
organizations. Licenses are granted to research groups, departments,
institutes etc. through a contact person by a signed a license
agreement. There is no need to get a new license for each additional
user or computer within the same organization. To request a free,
non-commercial user license, follow the steps below:</p>
<ul>
<li>Download and print the license agreement for
non-commercial use (<a href="license/license.pdf">license.pdf </a>)</li>
<li>Fill in and sign the agreement form.</li>
<li>Send the completed agreement to the adress at the top of the form.</li>
<li>We appreciate if you include a short letter introducing yourself, your
organization and what you intend to use the software for. If you want
to receive back a copy signed by both parts then include a signed
copy. When we have recieved and accepted the agreement we will e-mail
you the login information that enables you to download the software
from our web server. To get access to the software
faster e-mail the agreement to the attention of Johan Åqvist at the Dept. of Cell &
Molecular Biology. You must still send the
agreement by post to the Department of Cell and
Molecular Biology at Uppsala University.
</li>
</ul>
<h2 class="content-subhead">For commercial use</h2>
<p>We are working on a licencing scheme for commercial users, involving a
license fee. Please send inquiries to Johan Åqvist, introducing
yourself and your company. The evaluation version is of course
available also to prospective commercial users.</p> -->
<h2 class="content-subhead"><span id="support">Support</span></h2>
<p>We have no resources to support users of Q but of course we
appreciate a dialogue with you as a user. Particularly, we are anxious
to hear from you in the (hopefully unlikely?) case that you discover a
bug in the program. If time permits, we may also be able to answer
other questions, e. g. about using the program, simulation procedures,
or compilation. If you have questions about Q regarding licenses,
send these directly to Johan Åqvist (<script type="text/javascript">
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).</p>
<h2 class="content-subhead"><span id="mailinglist">Q-user mailing list</span></h2>
<p>The Q-users mailing list is hosted at google-groups:</p>
<p><a href="https://groups.google.com/forum/#!forum/qmoldyn">qmolecular-dynamics</a></p>
<p>To be included in the list please send a request to: qmoldyn@googlegroups.com</p>
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