Update model.html

wiki/pages/model.html

@@ -821,12 +821,74 @@
                     process
                 </p>
                 <div class="image-container">
-                    <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/density.png" alt="density"
+                    <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/mds-result.png" alt="density"
                         class="shadowed-image" style="width: 50%; max-width: 500px;">
                 </div>
                 <p style="text-align: center; font-size: 0.9em; margin-top: 10px;">fig 12 Results of the molecular
                     dynamics simulations
                 </p>
+                <h3>5. Post-Processing and Analysis</h3>
+
+                <ul>
+                    <li>After the completion of molecular dynamics simulations, detailed post-processing and analysis of
+                        the data is a key step in understanding the behavior of molecular systems. This section will
+                        demonstrate the use of GROMACS tools to analyze trajectory data, and visualize it using VMD and
+                        PyMOL.</li>
+                </ul>
+
+                <h4>1. Trajectory Analysis:</h4>
+
+                <p>To gain deeper insights into the interactions between muscone and the receptor, visualization tools
+                    are used to make the simulation process intuitive, identifying key interaction sites and structural
+                    changes.</p>
+
+                <ul>
+                    <li>Using the <code>gmx trjconv</code> tool, the calculated trajectory data is centered and periodic
+                        boundary conditions are removed, generating the centered trajectory file
+                        <code>md_0_10_center.xtc</code> and its initial frame <code>start.pdb</code>.
+                    </li>
+                </ul>
+
+                <pre><code>gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center -pbc mol -ur compact
+                #1 0
+                gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o start.pdb -dump 0
+                #0
+                </code></pre>
+
+                <ul>
+                    <li>In PyMOL, key interactions of the protein-ligand system can be visualized through selection and
+                        rotation commands, identifying important residues and binding pockets that play significant
+                        roles during the simulation process.</li>
+                </ul>
+
+                <pre><code># Pymol
+                select water, resn SOL
+                select ions, resn CL
+                select protein, not water and not ions
+                select ligand, resn MUS
+                deselect
+                cmd.rotate('x', 45)
+                cmd.rotate('y', 45)
+                </code></pre>
+
+                <img src="start.png" alt="start.pdb">
+
+                <ul>
+                    <li>Finally, generate a fitted trajectory file suitable for analysis and animation production.</li>
+                </ul>
+
+                <pre><code>gmx trjconv -s md_0_10.tpr -f md_0_10_center.xtc -o md_0_10_fit.xtc -fit rot+trans
+                #4 0
+                gmx trjconv -s md_0_10.tpr -f md_0_10_fit.xtc -o traj.pdb -dt 10
+                #0
+                </code></pre>
+
+                <div class="image-container">
+                    <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/muscure.gif" alt="Trajectory Analysis"
+                        class="shadowed-image" style="width: 50%; max-width: 500px;">
+                </div>
+                <p style="text-align: center; font-size: 0.9em; margin-top: 10px;">fig 13 Trajectory Analysis
+                </p>
         </div>
     </div>