diff --git a/wiki/pages/model.html b/wiki/pages/model.html index 5fa5dff7c7d3361cc586731327f6ec3313d510e2..2db59995c4643ea05a397f3f3d8dff2cb9bf64d3 100644 --- a/wiki/pages/model.html +++ b/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 Ã…. 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>