<!-- manual page source format generated by PolyglotMan v3.2, --> <!-- available at http://polyglotman.sourceforge.net/ --> <html> <head> <title>obminimize</title> </head> <body bgcolor='white'> <a href='#toc'>Table of Contents</a><p> <h2><a name='sect0' href='#toc0'>Name</a></h2> <p> <b>obminimize</b> -- optimize the geometry, minimize the energy for a molecule <p> <h2><a name='sect1' href='#toc1'><b>Synopsis</b></a></h2> <p> <b>obminimize</b> [<i>OPTIONS</i>] <i>filename</i> <p> <h2><a name='sect2' href='#toc2'><b>Description</b></a></h2> <p> The obminimize tool can be used to minimize the energy for molecules inside (multi-)molecule files (e.g., MOL2, etc.) <p> <h2><a name='sect3' href='#toc3'><b>Options</b></a></h2> <p> If no filename is given, obminimize will give all options including the available forcefields. <p> <dl> <dt><b>-n</b> <i>steps</i></dt></dt> <dd> Specify the maximum number of steps (default=2500) <p></dd> <dt><b>-cg</b> </dt></dt> <dd>Use conjugate gradients algorithm (default) <p></dd> <dt><b>-sd</b> </dt></dt> <dd>Use steepest descent algorithm <p></dd> <dt><b>-c</b> <i>criteria</i></dt></dt> <dd> Set convergence criteria (default=1e-6) <p></dd> <dt><b>-ff</b> <i>forcefield</i></dt></dt> <dd> Select the forcefield <p></dd> </dl> <h2><a name='sect4' href='#toc4'><b>Examples</b></a></h2> <p> View the possible options, including available forcefields:<br> <pre>obminimize</pre> <p><p> Minimize the energy for the molecule(s) in file test.mol2:<br> <pre>obminimize test.mol2</pre> <p><p> Minimize the energy for the molecule(s) in file test.mol2 using the Ghemical forcefield:<br> <pre>obminimize -ff Ghemical test.mol2</pre> <p><p> Minimize the energy for the molecule(s) in file test.mol2 by taking at most 300 geometry optimization steps<br> <pre>obminimize -n 300 test.mol2</pre> <p><p> Minimize the energy for the molecule(s) in file test.mol2 using the steepest descent algorithm and convergence criteria 1e-5:<br> <pre>obminimize -sd -c 1e-5 test.mol2</pre> <p> <h2><a name='sect5' href='#toc5'><b>See</b> <b>Also</b></a></h2> <p> <a href='babel.html'>babel(1)</a> , <a href='obenergy.html'>obenergy(1)</a> , <a href='obrotamer.html'>obrotamer(1)</a> . <p><p> The web pages for Open Babel can be found at: <<b><a href="http://openbabel.org/">http://openbabel.org/</a></b>> <p><p> The web pages for Open Babel Molecular Mechanics can be found at: <<b><a href="http://openbabel.org/wiki/Molecular_mechanics">http://openbabel.org/wiki/Molecular_mechanics</a></b>> <p> <h2><a name='sect6' href='#toc6'><b>Authors</b></a></h2> <p> The minimize program was contributed by Tim Vandermeersch. <p><p> Open Babel is developed by a cast of many, including currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see <<b><a href="http://openbabel.org/wiki/THANKS">http://openbabel.org/wiki/THANKS</a></b>> <p> <h2><a name='sect7' href='#toc7'><b>Copyright</b></a></h2> <p> Copyright (C) 2007 by Tim Vandermeersch. <p><p> This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License. <p><p> This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. <p> <hr><p> <a name='toc'><b>Table of Contents</b></a><p> <ul> <li><a name='toc0' href='#sect0'>Name</a></li> <li><a name='toc1' href='#sect1'>Synopsis</a></li> <li><a name='toc2' href='#sect2'>Description</a></li> <li><a name='toc3' href='#sect3'>Options</a></li> <li><a name='toc4' href='#sect4'>Examples</a></li> <li><a name='toc5' href='#sect5'>See Also</a></li> <li><a name='toc6' href='#sect6'>Authors</a></li> <li><a name='toc7' href='#sect7'>Copyright</a></li> </ul> </body> </html>
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