CHARMM tutorial - Recent changes [en]

CHARMM tutorial - Recent changes [en] http://www.charmmtutorial.org/index.php/Special:RecentChanges Track the most recent changes to the wiki in this feed. en MediaWiki 1.15.5-1 Wed, 08 Sep 2010 04:01:26 GMT MediaWiki:Sidebar http://www.charmmtutorial.org/index.php?title=MediaWiki:Sidebar&diff=819&oldid=prev http://www.charmmtutorial.org/index.php?title=MediaWiki:Sidebar&diff=819&oldid=prev <p>Fix links</p> Sat, 04 Sep 2010 04:09:46 GMT Tim http://www.charmmtutorial.org/index.php/MediaWiki_talk:Sidebar Main Page http://www.charmmtutorial.org/index.php?title=Main_Page&diff=818&oldid=prev http://www.charmmtutorial.org/index.php?title=Main_Page&diff=818&oldid=prev <p>Add link for where to post comments</p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 01:43, 4 September 2010</td> </tr> <tr><td colspan='4' align='center' class='diff-multi'>(One intermediate revision not shown)</td></tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><big>'''MediaWiki has been successfully installed.'''</big></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">==CHARMM (Chemistry at HARvard Macromolecular Mechanics) Tutorial==</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Consult the </del>[<del class="diffchange diffchange-inline">http</del>:<del class="diffchange diffchange-inline">//meta</del>.<del class="diffchange diffchange-inline">wikimedia.org</del>/<del class="diffchange diffchange-inline">wiki/Help:Contents User's Guide] for information on using the wiki software.</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[<ins class="diffchange diffchange-inline">[Image</ins>:<ins class="diffchange diffchange-inline">frontpage3</ins>.<ins class="diffchange diffchange-inline">png]]<br </ins>/<ins class="diffchange diffchange-inline">></ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">== Getting started ==</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">This tutorial was created by several [[Credits|contributors]] from different research groups.</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">* </del>[http://www.<del class="diffchange diffchange-inline">mediawiki</del>.org/<del class="diffchange diffchange-inline">wiki/Manual</del>:<del class="diffchange diffchange-inline">Configuration_settings Configuration settings list</del>]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br />Tutorial available online at: <br /></ins>[http://www.<ins class="diffchange diffchange-inline">charmmtutorial</ins>.org/ <ins class="diffchange diffchange-inline">http</ins>:<ins class="diffchange diffchange-inline">//www.charmmtutorial.org</ins>]<ins class="diffchange diffchange-inline"><br /><br />CHARMMing available at: <br /></ins>http://www.<ins class="diffchange diffchange-inline">charmming</ins>.org<ins class="diffchange diffchange-inline"><br </ins>/<ins class="diffchange diffchange-inline">><br </ins>/<ins class="diffchange diffchange-inline">>CHARMM Documentation and Forums available at</ins>: <ins class="diffchange diffchange-inline"><br />http://www.charmm.org</ins></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">* [</del>http://www.<del class="diffchange diffchange-inline">mediawiki</del>.org/<del class="diffchange diffchange-inline">wiki</del>/<del class="diffchange diffchange-inline">Manual</del>:<del class="diffchange diffchange-inline">FAQ MediaWiki FAQ]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">* </del>[http://<del class="diffchange diffchange-inline">lists</del>.<del class="diffchange diffchange-inline">wikimedia</del>.org/<del class="diffchange diffchange-inline">mailman</del>/<del class="diffchange diffchange-inline">listinfo</del>/<del class="diffchange diffchange-inline">mediawiki-announce MediaWiki release mailing list</del>]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">If you have any comments or suggestions for this tutorial, please post them on the </ins>[http://<ins class="diffchange diffchange-inline">www</ins>.<ins class="diffchange diffchange-inline">charmm</ins>.org/<ins class="diffchange diffchange-inline">ubbthreads-7-5-5</ins>/<ins class="diffchange diffchange-inline">ubbthreads.php?ubb=postlist&Board=37&page=1 CHARMMing discussion board] of the [http:</ins>/<ins class="diffchange diffchange-inline">/www.charmm.org/ubbthreads CHARMM forums</ins>]<ins class="diffchange diffchange-inline">.</ins></div></td></tr>   </table> Sat, 04 Sep 2010 01:43:57 GMT Tim http://www.charmmtutorial.org/index.php/Talk:Main_Page CHARMM tutorial:About http://www.charmmtutorial.org/index.php?title=CHARMM_tutorial:About&diff=816&oldid=prev http://www.charmmtutorial.org/index.php?title=CHARMM_tutorial:About&diff=816&oldid=prev <p>get credits link right!</p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 01:41, 4 September 2010</td> </tr> <tr><td colspan='4' align='center' class='diff-multi'>(3 intermediate revisions not shown)</td></tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==CHARMM (Chemistry at HARvard Macromolecular Mechanics) Tutorial==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==CHARMM (Chemistry at HARvard Macromolecular Mechanics) Tutorial==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">===Rishi P. Singh, Benjamin T. Miller, Jeffery Klauda, Xiongwu Wu, and H. Lee Woodcock===</del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:frontpage3.png]]<br /></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:frontpage3.png]]<br /></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Image:ourlogo.png|50%|NHLBI Logo]]<br /></del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Laboratory of Computational Biology <br />NIH, NHLBI <br />5635 Fishers Lane Suite T900</del>. <del class="diffchange diffchange-inline">MSC 8014 <br />Bethesda, MD 20892-8014 <br />http://www.lobos.nih.gov/cbs<br /></del><br />Tutorial available online at: <br />[http://www.charmmtutorial.org/ http://www.charmmtutorial.org]<br /><br />CHARMMing available at: <br />http://www.charmming.org<br /><br />CHARMM Documentation and Forums available at: <br />http://www.charmm.org</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">This tutorial was created by several [[Credits|contributors]] from different research groups</ins>.</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><br />Tutorial available online at: <br />[http://www.charmmtutorial.org/ http://www.charmmtutorial.org]<br /><br />CHARMMing available at: <br />http://www.charmming.org<br /><br />CHARMM Documentation and Forums available at: <br />http://www.charmm.org</div></td></tr>   </table> Sat, 04 Sep 2010 01:41:36 GMT Tim http://www.charmmtutorial.org/index.php/CHARMM_tutorial_talk:About The Energy Function http://www.charmmtutorial.org/index.php?title=The_Energy_Function&diff=812&oldid=prev http://www.charmmtutorial.org/index.php?title=The_Energy_Function&diff=812&oldid=prev <p><span class="autocomment">The force field terms: </span> </p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 22:52, 3 September 2010</td> </tr> <tr><td colspan='4' align='center' class='diff-multi'>(4 intermediate revisions not shown)</td></tr><tr><td colspan="2" class="diff-lineno">Line 21:</td> <td colspan="2" class="diff-lineno">Line 21:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>where <math>U_{\mathit{bonded}}</math> consists of the following terms,</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>where <math>U_{\mathit{bonded}}</math> consists of the following terms,</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><math>U_{\mathit{bonded}}=U_{\mathit{bond}}+U_{\mathit{angle}}+U_{\mathit{UB}}+U_{\mathit{dihedral}}</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><math>U_{\mathit{bonded}} = U_{\mathit{bond}} + U_{\mathit{angle}} + U_{\mathit{UB}} + U_{\mathit{dihedral}}</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>+U_{\mathit{improper}}+U_{\mathit{CMAP}}</math></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>+U_{\mathit{improper}}+U_{\mathit{CMAP}}</math></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>   </table> Fri, 03 Sep 2010 22:52:31 GMT Tim http://www.charmmtutorial.org/index.php/Talk:The_Energy_Function