http://rxnkin.usc.es/index.php?action=history&feed=atom&title=AutoMeKin%3AAbout 2026-05-05T16:33:49Z Revision history for this page on the wiki MediaWiki 1.32.0 http://rxnkin.usc.es/index.php?title=AutoMeKin:About&diff=123&oldid=prev 2019-04-14T16:56:35Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:56, 14 April 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>AutoMeKin is a computer program that has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion. AutoMeKin obtains transition state guess structures from trajectory simulations of the highly vibrationally excited species. From the obtained TS structures, minima and product fragments are determined following the intrinsic reaction coordinate. Finally, having determined the stationary points, the reaction network is constructed and the kinetics is solved<del class="diffchange diffchange-inline">. The program is interfaced with MOPAC2016 and Gaussian 09 (G09)</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>AutoMeKin is a computer program that has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion. AutoMeKin obtains transition state guess structures from trajectory simulations of the highly vibrationally excited species. From the obtained TS structures, minima and product fragments are determined following the intrinsic reaction coordinate. Finally, having determined the stationary points, the reaction network is constructed and the kinetics is solved.  </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Main Page]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Main Page]]</div></td></tr> </table>

Wikiadmin http://rxnkin.usc.es/index.php?title=AutoMeKin:About&diff=122&oldid=prev 2019-04-14T16:56:20Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:56, 14 April 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>AutoMeKin has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion. AutoMeKin obtains transition state <del class="diffchange diffchange-inline">(TS) </del>guess structures from trajectory simulations of the highly vibrationally excited species. From the obtained TS structures, minima and product fragments are determined following the intrinsic reaction coordinate <del class="diffchange diffchange-inline">(IRC)</del>. <del class="diffchange diffchange-inline">Then</del>, <del class="diffchange diffchange-inline">with all </del>the stationary points, the reaction network is constructed<del class="diffchange diffchange-inline">. Finally, </del>the kinetics is solved <del class="diffchange diffchange-inline">using the Kinetic Monte Carlo (KMC) method</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>AutoMeKin <ins class="diffchange diffchange-inline">is a computer program that </ins>has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion. AutoMeKin obtains transition state guess structures from trajectory simulations of the highly vibrationally excited species. From the obtained TS structures, minima and product fragments are determined following the intrinsic reaction coordinate. <ins class="diffchange diffchange-inline">Finally</ins>, <ins class="diffchange diffchange-inline">having determined </ins>the stationary points, the reaction network is constructed <ins class="diffchange diffchange-inline">and </ins>the kinetics is solved. The program is interfaced with MOPAC2016 and Gaussian 09 (G09).</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The program is interfaced with MOPAC2016 and Gaussian 09 (G09).</div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Details of the method are described in these two publications: [http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract 1]</del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">[http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract 2]</del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Users are encouraged to read the [http://forge.cesga.es/frs/?group_id=77&amp;release_id=21 tutorial], which is thought to guide you through the various steps necessary to predict reaction mechanisms and kinetics of unimolecular decompositions. To facilitate the presentation, we consider, as an example, the decomposition of formic acid (FA).</del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 16.04.3 LTS</del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Main Page]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Main Page]]</div></td></tr> </table>

Wikiadmin http://rxnkin.usc.es/index.php?title=AutoMeKin:About&diff=119&oldid=prev 2019-04-14T16:54:14Z

<p>Created page with &quot;AutoMeKin has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion. AutoMeKin obtains transition state (TS) guess structures from traje...&quot;</p> <p><b>New page</b></p><div>AutoMeKin has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion. AutoMeKin obtains transition state (TS) guess structures from trajectory simulations of the highly vibrationally excited species. From the obtained TS structures, minima and product fragments are determined following the intrinsic reaction coordinate (IRC). Then, with all the stationary points, the reaction network is constructed. Finally, the kinetics is solved using the Kinetic Monte Carlo (KMC) method.<br /> The program is interfaced with MOPAC2016 and Gaussian 09 (G09).<br /> <br /> Details of the method are described in these two publications: [http://onlinelibrary.wiley.com/doi/10.1002/jcc.23790/abstract 1]<br /> [http://pubs.rsc.org/en/content/articlelanding/2015/cp/c5cp02175h#!divAbstract 2]<br /> <br /> Users are encouraged to read the [http://forge.cesga.es/frs/?group_id=77&amp;release_id=21 tutorial], which is thought to guide you through the various steps necessary to predict reaction mechanisms and kinetics of unimolecular decompositions. To facilitate the presentation, we consider, as an example, the decomposition of formic acid (FA).<br /> <br /> The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 16.04.3 LTS<br /> <br /> [[Main Page]]</div>

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