Bug fixes

biobb_wf_protein-complex_md_setup/html/biobb_Protein-Complex_MDsetup_tutorial.web.html

@@ -9787,18 +9787,18 @@ <h3 id="Step-3:-Visualizing-the-generated-dehydrated-trajectory.">Step 3: Visual
 <p><a id="output"></a></p>
 <h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">¶</a></h2><p>Important <strong>Output files</strong> generated:</p>
 <ul>
-<li>{{output_md_gro}}: <strong>Final structure</strong> (snapshot) of the MD setup protocol.</li>
-<li>{{output_md_trr}}: <strong>Final trajectory</strong> of the MD setup protocol.</li>
-<li>{{output_md_cpt}}: <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
-<li>{{output_gppmd_tpr}}: <strong>Final tpr file</strong>, GROMACS portable binary run input file. This file contains the starting structure of the <strong>MD setup free MD simulation step</strong>, together with the molecular topology and all the simulation parameters. It can be used to <strong>extend</strong> the simulation.</li>
-<li>{{output_genion_top_zip}}: <strong>Final topology</strong> of the MD system. It is a compressed zip file including a <strong>topology file</strong> (.top) and a set of auxiliary <strong>include topology</strong> files (.itp).</li>
-</ul>
-<p><strong>Analysis</strong> (MD setup check) output files generated:</p>
-<ul>
-<li>{{output_rms_first}}: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
-<li>{{output_rms_exp}}: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
-<li>{{output_rgyr}}: <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
-</ul>
+  <li>3HTB_JZ4_md.gro: <strong>Final structure</strong> (snapshot) of the MD setup protocol.</li>
+  <li>3HTB_JZ4_md.trr: <strong>Final trajectory</strong> of the MD setup protocol.</li>
+  <li>3HTB_JZ4_md.cpt: <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
+  <li>3HTB_JZ4_gppmd.tpr: <strong>Final tpr file</strong>, GROMACS portable binary run input file. This file contains the starting structure of the <strong>MD setup free MD simulation step</strong>, together with the molecular topology and all the simulation parameters. It can be used to <strong>extend</strong> the simulation.</li>
+  <li>3HTB_JZ4_genion_top.zip: <strong>Final topology</strong> of the MD system. It is a compressed zip file including a <strong>topology file</strong> (.top) and a set of auxiliar <strong>include topology</strong> files (.itp).</li>
+  </ul>
+  <p><strong>Analysis</strong> (MD setup check) output files generated:</p>
+  <ul>
+  <li>3HTB_JZ4_rms_first.xvg: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
+  <li>3HTB_JZ4_rms_exp.xvg: <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
+  <li>3HTB_JZ4_rgyr.xvg: <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
+  </ul>
 </div>
 </div>
 </div>