<![CDATA[
<BODY>
<P>
<TABLE BORDER="0" WIDTH="80%">
<TR>
<TD><IMG SRC="Qlogo2.gif" WIDTH="240" HEIGHT="287" ALIGN="BOTTOM" BORDER="0"></TD>
<TD VALIGN="BOTTOM">
<H1><FONT SIZE="7">Q - our Molecular dynamics program</FONT>
</TD>
</TR>
</TABLE>
Q is a molecular dynamics package designed for free energy calculations in biomolecular systems.
<H2>Contents</H2>
<P>
<TABLE BORDER="0" WIDTH="75%">
<TR VALIGN="TOP">
<TD VALIGN="TOP">1</TD>
<TD><A HREF="#intro">Introduction</A></TD>
<TD> </TD>
</TR>
<TR>
<TD>2</TD>
<TD><A HREF="download/">Download</A> the program </TD>
<TD>for licenced users only!</TD>
</TR>
<TR>
<TD>3</TD>
<TD><A HREF="#doc">Documentation</A></TD>
<TD> </TD>
</TR>
<TR>
<TD>4</TD>
<TD><A HREF="#eval">Evaluation version</A></TD>
<TD> </TD>
</TR>
<TR>
<TD>5</TD>
<TD><A HREF="samples/">Examples</A></TD>
<TD>updated July 9, 1999</TD>
</TR>
<TR>
<TD>6</TD>
<TD><A HREF="download/ff/">Force field files</A></TD>
<TD>for licenced users only!</TD>
</TR>
<TR>
<TD>7</TD>
<TD><A HREF="#obtain">Obtaining a license</A></TD>
<TD> </TD>
</TR>
<TR>
<TD>8</TD>
<TD><A HREF="#support">Support</A></TD>
<TD> </TD>
</TR>
</TABLE>
<H2>Introduction</H2>
<P><A NAME="intro"></A>The first version was written by Johan Åqvist in 1996. At present, we use the fourth
major version of the program developed 1998 by John Marelius, Johan Åqvist and Karin Kolmodin. <BR>
Some general features of the program:
<UL>
<LI>Designed for free energy calculations:
<UL>
<LI><A HREF="../projects.html#EVB">Empirical Valence Bond (EVB) method</A> for reaction free energy profiles.
<LI><A HREF="../projects.html#FEP">Free Energy Perturbation.</A>
<LI><A HREF="../projects.html#LIE">Linear Interaction Energy (LIE) method</A> for receptor-ligand binding free
energies.
</UL>
<LI>Simulate any number of atoms (as many as your computer can handle).
<LI>Solvate molecules in a sphere of water molecules using boundary conditions designed to reproduce density, and
interaction potentials of bulk water.
<LI>Easier to use than most MD packages: no fixed-format files, input file formats designed to be readable and
writable by humans.
<LI>Several popular <A HREF="download/ff/">force fields</A> can be used:
<UL>
<LI>GROMOS87
<LI>GROMOS96
<LI>Amber/OPLS
<LI>AMBER95
<LI>CHARMM v.22
</UL>
<LI>Portable code that runs on many platforms:
<UL>
<LI>Windows NT 4 (Alpha)
<LI>Windows NT 4 (x86), Windows95, Windows98
<LI>Digital UNIX 4
<LI>SGI Irix 6
<LI>Linux
</UL>
</UL>
<H2><A NAME="eval"></A>Evaluation version</H2>
<P>If you want to try Q before requesting a licence, 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 optimisations disabled and therefore run at less
than 20% of the speed of the optimised programs. Only Gromos87 force field files are included in the kit.
<UL>
<LI><A HREF="eval/Qeval_Win32_x86.zip">Download evaluation kit</A>
</UL>
<P>An example of binding free energy calculation is included.
<H2><A NAME="doc"></A>Documentation</H2>
<P>The manual is distributed in PDF format. You need <A HREF="http://www.adobe.com/prodindex/acrobat/readstep.html#reader"
target="_parent">Acrobat Reader</A> from <A HREF="http://www.adobe.com" target="_parent">Adobe</A> to view and
print it.
<UL>
<LI><A HREF="qman4.pdf">Q manual in PDF format</A>
</UL>
<P>The latest changes are briefly documented in the version history files:
<UL>
<LI><A HREF="Qdyn_history.txt">Qdyn version history</A>
<LI><A HREF="Qprep_history.txt">Qprep version history</A>
<LI><A HREF="Qfep_history.txt">Qfep version history</A>
</UL>
<H2><A NAME="obtain"></A>Obtaining the program</H2>
<P>Our policy is to distribute the program, complete with source code, without charge to academic institutions
and to other non-profit organisations. We are working on a licencing scheme for commercial users, involving a licence
fee. <BR>
To obtain the license, send an e-mail message to <A HREF="mailto:aqvist@alpha2.bmc.uu.se">Johan Åqvist</A>
introducing yourself and your organisation. We are also curious to know what you plan to use the program for.
<H2><A NAME="support"></A>Support</H2>
<P>We have no resources dedicated to support users of Q, but of course we appreciate a dialogue with you as a user.
Particularly, we are anxoius 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. <BR>
We might consider offering support as part of the license scheme. <BR>
<A HREF="mailto:john@alpha2.bmc.uu.se">John Marelius</A> will handle the support matters. <BR>
</BODY>
]]>