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<!-- Copyright 2008 Nanorex, Inc. See LICENSE file for details. -->
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<title>
GROMACS 3.3.2 + HDF5 Patch #2
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<h1>GROMACS 3.3.2 + HDF5 Patch #2</h1>
<a href="http://www.gromacs.org/">GROMACS</a> (GMX) is an extremely high performance, open source, and cross-platform package used to perform molecular dynamics simulation of systems with hundreds to millions of particles. NE1 currently uses GROMACS+HDF5 as an energy minimization engine option. The +HDF5 comes from our experimental <a href="http://hdf.ncsa.uiuc.edu/HDF5/">HDF5</a>-based simulation results file format augmentation. The HDF5 file format won't affect non-HDF5 GMX operation. Also included with the binary installers is <a href="http://mcpp.sourceforge.net/"><tt>mcpp</tt></a>, a free, open source, portable C preprocessor. A C preprocessor is required for GROMACS use, so we've included one since some platforms don't come with one.
<p>
This is GROMACS 3.3.2 + HDF5 Patch #2 as of April 25, 2008.
<p>
Click the following links or visit the official <a href="http://www.nanoengineer-1.com/GROMACS_HDF5/">GROMACS_HDF5</a> page to learn more about GROMACS+HDF5:
<ul>
<li><a href="#InstallationInstructions">Installation Instructions</a>
<li><a href="#Copyright">Copyrights and Licensing</a>
</ul>
<a name="InstallationInstructions"></a>
<h2>Installation Instructions</h2>
<h3>Windows</h3>
Run the GROMACS+HDF5 self-extracting installer "GROMACS_3.3.2+HDF5_p2.exe".
<h3>Mac OS X</h3>
Run the GROMACS+HDF5 self-extracting installer "GROMACS_3.3.2+HDF5_p2.dmg".
<h3>Linux and Developers</h3>
GROMACS+HDF5 must be compiled from sources for Linux users and developers. Download the GROMACS+HDF5 source distribution "GROMACS_3.3.2+HDF5_p2.tar.gz" and follow the instructions here: <a href="http://www.nanoengineer-1.net/mediawiki/index.php?title=The_GROMACS_Package_for_NE1#Building_and_Installing_GROMACS.2BHDF5">Building and Installing GROMACS+HDF5</a>
<h3>Post-install Notes</h3>
If you have not installed this from the NanoEngineer-1 Suite installer you will have to modify your preferences to enable NanoEngineer-1 to use this plugin.
<ol>
<li> Launch NanoEngineer-1
<li> Choose Tools -> Preferences -> Plug-ins
<li> Check the box for GROMACS and input the full path to the mdrun executable including its file name. For example, on Windows it may be C:\GROMACS_3.3.2+HDF5_p2\bin\mdrun.exe)
<li> Check the box for cpp and input the full path to the mcpp executable including its file name. For example, on Windows it may be C:\GROMACS_3.3.2+HDF5_p2\MCPP\bin\mcpp.exe)
<li> Click Ok.
</ol>
<a name="Copyright"></a>
<h2>Copyrights and Licensing</h2>
GROMACS is <i>Free Software</i>, available under the <a href="http://www.gnu.org/licenses/licenses.html#GPL">GNU General Public License</a>.
<p>
Our modifications to the GROMACS code are Copyright 2007-2008 Nanorex, Inc. and fall under GROMACS's GPL license.
<p>
See source/HDF5_COPYING for HDF5 copyright and licensing details.
<p>
<tt>mcpp</tt> is open source software released under a BSD-style license. See MCPP/LICENSE for details.
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