Update model.html

wiki/pages/model.html

@@ -815,14 +815,14 @@
                 </code></pre>
                 <div class="image-container">
                     <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/mds.png" alt="MDS"
-                        class="shadowed-image" style="width: 50%; max-width: 500px;">
+                        class="shadowed-image" style="width: 100%; max-width: 1000px;">
                 </div>
                 <p style="text-align: center; font-size: 0.9em; margin-top: 10px;">fig 11 Molecular dynamics simulation
                     process
                 </p>
                 <div class="image-container">
                     <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;">
+                        class="shadowed-image" style="width: 100%; max-width: 1000px;">
                 </div>
                 <p style="text-align: center; font-size: 0.9em; margin-top: 10px;">fig 12 Results of the molecular
                     dynamics simulations
@@ -889,6 +889,48 @@
                 </div>
                 <p style="text-align: center; font-size: 0.9em; margin-top: 10px;">fig 13 Trajectory Analysis
                 </p>
+                <h4>2. RMSD (Root Mean Square Deviation) Analysis</h4>
+
+                <ul>
+                    <li>RMSD provides a fundamental metric for measuring structural deviation during the simulation
+                        process. By calculating the deviation of structures at different time points, it is possible to
+                        assess the stability of the system.</li>
+                </ul>
+
+                <pre><code>gmx distance -s md_0_10.tpr -f md_0_10_center.xtc -select 'resname "MUS" and name O plus resid 51 and name NH1' -oall
+                gmx make_ndx -f em.gro -o index.ndx
+                > 13 & a O  
+                > 1 & r 51 & a NH1
+                > 1 & r 51 & a CZ
+                > 20 | 21 | 22
+                > q
+                gmx angle -f md_0_10_center.xtc -n index.ndx -ov angle.xvg 
+                gmx make_ndx -f em.gro -n index.ndx
+                > 13 & ! a H*
+                > name MUS_Heavy
+                > q
+                gmx rms -s em.tpr -f md_0_10_center.xtc -n index.ndx -tu ns -o rmsd_mus.xvg
+                
+                xmgrace rmsd_mus.xvg
+                dit xvg_show -f rmsd_mus.xvg
+                xmgrace rmsd_mus.xvg
+                </code></pre>
+
+                <ul>
+                    <li>From the RMSD curve, it can be observed that the system stabilizes after approximately 1
+                        nanosecond, with a fluctuation range of around 1.3 Å. This indicates that the structures of the
+                        protein and ligand remained relatively stable throughout the simulation process, with no
+                        significant conformational changes occurring, supporting the potential biological significance
+                        of the results.</li>
+                </ul>
+                <div class="image-container">
+                    <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/rmsd.png" alt="RMSD"
+                        class="shadowed-image" style="width: 50%; max-width: 500px;">
+                </div>
+                <p style="text-align: center; font-size: 0.9em; margin-top: 10px;">fig 14 RMSD Analysis
+                </p>
+
+                <img src="rmsd.png" alt="RMSD Plot">
         </div>
     </div>