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th2ch-g committed Feb 27, 2024
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<nav id="sidebar" class="sidebar" aria-label="Table of contents">
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<ol class="chapter"><li class="chapter-item expanded affix "><a href="index.html">PaCS-Toolkit User Guide</a></li><li class="chapter-item expanded "><a href="quickstart.html"><strong aria-hidden="true">1.</strong> Quick Start</a></li><li class="chapter-item expanded "><a href="install.html"><strong aria-hidden="true">2.</strong> Install</a></li><li class="chapter-item expanded "><a href="mdrun.html"><strong aria-hidden="true">3.</strong> mdrun</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/overview.html"><strong aria-hidden="true">3.1.</strong> Overview</a></li><li class="chapter-item expanded "><a href="mdrun/basic.html"><strong aria-hidden="true">3.2.</strong> Basic</a></li><li class="chapter-item expanded "><a href="mdrun/simulator.html"><strong aria-hidden="true">3.3.</strong> Simulator</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer.html"><strong aria-hidden="true">3.4.</strong> Analyzer</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/analyzer/rmsd.html"><strong aria-hidden="true">3.4.1.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/target.html"><strong aria-hidden="true">3.4.2.</strong> target</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/dissociation.html"><strong aria-hidden="true">3.4.3.</strong> dissociation</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/association.html"><strong aria-hidden="true">3.4.4.</strong> association</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/a_d.html"><strong aria-hidden="true">3.4.5.</strong> a_d</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/ee.html"><strong aria-hidden="true">3.4.6.</strong> ee</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/template.html"><strong aria-hidden="true">3.4.7.</strong> template</a></li></ol></li><li class="chapter-item expanded "><a href="mdrun/inputfile.html"><strong aria-hidden="true">3.5.</strong> Input file</a></li><li class="chapter-item expanded "><a href="mdrun/reference.html"><strong aria-hidden="true">3.6.</strong> Reference</a></li></ol></li><li class="chapter-item expanded "><a href="rmmol.html"><strong aria-hidden="true">4.</strong> rmmol</a></li><li class="chapter-item expanded "><a href="rmfile.html"><strong aria-hidden="true">5.</strong> rmfile</a></li><li class="chapter-item expanded "><a href="fit.html"><strong aria-hidden="true">6.</strong> fit</a></li><li class="chapter-item expanded "><a href="genrepresent.html"><strong aria-hidden="true">7.</strong> genrepresent</a></li><li class="chapter-item expanded "><a href="gencom.html"><strong aria-hidden="true">8.</strong> gencom</a></li><li class="chapter-item expanded "><a href="genfeature.html"><strong aria-hidden="true">9.</strong> genfeature</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="genfeature/comdist.html"><strong aria-hidden="true">9.1.</strong> comdist</a></li><li class="chapter-item expanded "><a href="genfeature/comvec.html"><strong aria-hidden="true">9.2.</strong> comvec</a></li><li class="chapter-item expanded "><a href="genfeature/pca.html"><strong aria-hidden="true">9.3.</strong> pca</a></li><li class="chapter-item expanded "><a href="genfeature/tica.html"><strong aria-hidden="true">9.4.</strong> tica</a></li><li class="chapter-item expanded "><a href="genfeature/rmsd.html"><strong aria-hidden="true">9.5.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="genfeature/xyz.html"><strong aria-hidden="true">9.6.</strong> xyz</a></li></ol></li><li class="chapter-item expanded "><a href="FAQ.html"><strong aria-hidden="true">10.</strong> FAQ</a></li></ol>
<ol class="chapter"><li class="chapter-item expanded affix "><a href="index.html">PaCS-Toolkit User Guide</a></li><li class="chapter-item expanded "><a href="quickstart.html"><strong aria-hidden="true">1.</strong> Quick Start</a></li><li class="chapter-item expanded "><a href="install.html"><strong aria-hidden="true">2.</strong> Install</a></li><li class="chapter-item expanded "><a href="mdrun.html"><strong aria-hidden="true">3.</strong> mdrun</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/overview.html"><strong aria-hidden="true">3.1.</strong> Overview</a></li><li class="chapter-item expanded "><a href="mdrun/basic.html"><strong aria-hidden="true">3.2.</strong> Basic</a></li><li class="chapter-item expanded "><a href="mdrun/simulator.html"><strong aria-hidden="true">3.3.</strong> Simulator</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer.html"><strong aria-hidden="true">3.4.</strong> Analyzer</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/analyzer/rmsd.html"><strong aria-hidden="true">3.4.1.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/target.html"><strong aria-hidden="true">3.4.2.</strong> target</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/dissociation.html"><strong aria-hidden="true">3.4.3.</strong> dissociation</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/association.html"><strong aria-hidden="true">3.4.4.</strong> association</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/a_d.html"><strong aria-hidden="true">3.4.5.</strong> a_d</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/ee.html"><strong aria-hidden="true">3.4.6.</strong> ee</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/template.html"><strong aria-hidden="true">3.4.7.</strong> template</a></li></ol></li><li class="chapter-item expanded "><a href="mdrun/inputfile.html"><strong aria-hidden="true">3.5.</strong> Input file</a></li><li class="chapter-item expanded "><a href="mdrun/reference.html"><strong aria-hidden="true">3.6.</strong> Reference</a></li></ol></li><li class="chapter-item expanded "><a href="rmmol.html"><strong aria-hidden="true">4.</strong> rmmol</a></li><li class="chapter-item expanded "><a href="rmfile.html"><strong aria-hidden="true">5.</strong> rmfile</a></li><li class="chapter-item expanded "><a href="fit.html"><strong aria-hidden="true">6.</strong> fit</a></li><li class="chapter-item expanded "><a href="genrepresent.html"><strong aria-hidden="true">7.</strong> genrepresent</a></li><li class="chapter-item expanded "><a href="gencom.html"><strong aria-hidden="true">8.</strong> gencom</a></li><li class="chapter-item expanded "><a href="genfeature.html"><strong aria-hidden="true">9.</strong> genfeature</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="genfeature/comdist.html"><strong aria-hidden="true">9.1.</strong> comdist</a></li><li class="chapter-item expanded "><a href="genfeature/comvec.html"><strong aria-hidden="true">9.2.</strong> comvec</a></li><li class="chapter-item expanded "><a href="genfeature/rmsd.html"><strong aria-hidden="true">9.3.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="genfeature/xyz.html"><strong aria-hidden="true">9.4.</strong> xyz</a></li></ol></li><li class="chapter-item expanded "><a href="FAQ.html"><strong aria-hidden="true">10.</strong> FAQ</a></li></ol>
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<nav id="sidebar" class="sidebar" aria-label="Table of contents">
<div class="sidebar-scrollbox">
<ol class="chapter"><li class="chapter-item expanded affix "><a href="index.html">PaCS-Toolkit User Guide</a></li><li class="chapter-item expanded "><a href="quickstart.html"><strong aria-hidden="true">1.</strong> Quick Start</a></li><li class="chapter-item expanded "><a href="install.html"><strong aria-hidden="true">2.</strong> Install</a></li><li class="chapter-item expanded "><a href="mdrun.html"><strong aria-hidden="true">3.</strong> mdrun</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/overview.html"><strong aria-hidden="true">3.1.</strong> Overview</a></li><li class="chapter-item expanded "><a href="mdrun/basic.html"><strong aria-hidden="true">3.2.</strong> Basic</a></li><li class="chapter-item expanded "><a href="mdrun/simulator.html"><strong aria-hidden="true">3.3.</strong> Simulator</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer.html"><strong aria-hidden="true">3.4.</strong> Analyzer</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/analyzer/rmsd.html"><strong aria-hidden="true">3.4.1.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/target.html"><strong aria-hidden="true">3.4.2.</strong> target</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/dissociation.html"><strong aria-hidden="true">3.4.3.</strong> dissociation</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/association.html"><strong aria-hidden="true">3.4.4.</strong> association</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/a_d.html"><strong aria-hidden="true">3.4.5.</strong> a_d</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/ee.html"><strong aria-hidden="true">3.4.6.</strong> ee</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/template.html"><strong aria-hidden="true">3.4.7.</strong> template</a></li></ol></li><li class="chapter-item expanded "><a href="mdrun/inputfile.html"><strong aria-hidden="true">3.5.</strong> Input file</a></li><li class="chapter-item expanded "><a href="mdrun/reference.html"><strong aria-hidden="true">3.6.</strong> Reference</a></li></ol></li><li class="chapter-item expanded "><a href="rmmol.html"><strong aria-hidden="true">4.</strong> rmmol</a></li><li class="chapter-item expanded "><a href="rmfile.html"><strong aria-hidden="true">5.</strong> rmfile</a></li><li class="chapter-item expanded "><a href="fit.html"><strong aria-hidden="true">6.</strong> fit</a></li><li class="chapter-item expanded "><a href="genrepresent.html"><strong aria-hidden="true">7.</strong> genrepresent</a></li><li class="chapter-item expanded "><a href="gencom.html"><strong aria-hidden="true">8.</strong> gencom</a></li><li class="chapter-item expanded "><a href="genfeature.html"><strong aria-hidden="true">9.</strong> genfeature</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="genfeature/comdist.html"><strong aria-hidden="true">9.1.</strong> comdist</a></li><li class="chapter-item expanded "><a href="genfeature/comvec.html"><strong aria-hidden="true">9.2.</strong> comvec</a></li><li class="chapter-item expanded "><a href="genfeature/pca.html"><strong aria-hidden="true">9.3.</strong> pca</a></li><li class="chapter-item expanded "><a href="genfeature/tica.html"><strong aria-hidden="true">9.4.</strong> tica</a></li><li class="chapter-item expanded "><a href="genfeature/rmsd.html"><strong aria-hidden="true">9.5.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="genfeature/xyz.html"><strong aria-hidden="true">9.6.</strong> xyz</a></li></ol></li><li class="chapter-item expanded "><a href="FAQ.html" class="active"><strong aria-hidden="true">10.</strong> FAQ</a></li></ol>
<ol class="chapter"><li class="chapter-item expanded affix "><a href="index.html">PaCS-Toolkit User Guide</a></li><li class="chapter-item expanded "><a href="quickstart.html"><strong aria-hidden="true">1.</strong> Quick Start</a></li><li class="chapter-item expanded "><a href="install.html"><strong aria-hidden="true">2.</strong> Install</a></li><li class="chapter-item expanded "><a href="mdrun.html"><strong aria-hidden="true">3.</strong> mdrun</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/overview.html"><strong aria-hidden="true">3.1.</strong> Overview</a></li><li class="chapter-item expanded "><a href="mdrun/basic.html"><strong aria-hidden="true">3.2.</strong> Basic</a></li><li class="chapter-item expanded "><a href="mdrun/simulator.html"><strong aria-hidden="true">3.3.</strong> Simulator</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer.html"><strong aria-hidden="true">3.4.</strong> Analyzer</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/analyzer/rmsd.html"><strong aria-hidden="true">3.4.1.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/target.html"><strong aria-hidden="true">3.4.2.</strong> target</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/dissociation.html"><strong aria-hidden="true">3.4.3.</strong> dissociation</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/association.html"><strong aria-hidden="true">3.4.4.</strong> association</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/a_d.html"><strong aria-hidden="true">3.4.5.</strong> a_d</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/ee.html"><strong aria-hidden="true">3.4.6.</strong> ee</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/template.html"><strong aria-hidden="true">3.4.7.</strong> template</a></li></ol></li><li class="chapter-item expanded "><a href="mdrun/inputfile.html"><strong aria-hidden="true">3.5.</strong> Input file</a></li><li class="chapter-item expanded "><a href="mdrun/reference.html"><strong aria-hidden="true">3.6.</strong> Reference</a></li></ol></li><li class="chapter-item expanded "><a href="rmmol.html"><strong aria-hidden="true">4.</strong> rmmol</a></li><li class="chapter-item expanded "><a href="rmfile.html"><strong aria-hidden="true">5.</strong> rmfile</a></li><li class="chapter-item expanded "><a href="fit.html"><strong aria-hidden="true">6.</strong> fit</a></li><li class="chapter-item expanded "><a href="genrepresent.html"><strong aria-hidden="true">7.</strong> genrepresent</a></li><li class="chapter-item expanded "><a href="gencom.html"><strong aria-hidden="true">8.</strong> gencom</a></li><li class="chapter-item expanded "><a href="genfeature.html"><strong aria-hidden="true">9.</strong> genfeature</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="genfeature/comdist.html"><strong aria-hidden="true">9.1.</strong> comdist</a></li><li class="chapter-item expanded "><a href="genfeature/comvec.html"><strong aria-hidden="true">9.2.</strong> comvec</a></li><li class="chapter-item expanded "><a href="genfeature/rmsd.html"><strong aria-hidden="true">9.3.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="genfeature/xyz.html"><strong aria-hidden="true">9.4.</strong> xyz</a></li></ol></li><li class="chapter-item expanded "><a href="FAQ.html" class="active"><strong aria-hidden="true">10.</strong> FAQ</a></li></ol>
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