+</ol>
+<hr>
+Advanced mode enables the user to change more parameters for each type of
+simulation. Separate examples are provided (use the <i>Load example data</i> button as
+in the Basic mode):
+<ol>
+<h4><li>
+Minimization of the P8MTCP1 disulfide-bonded helical hairpin miniprotein
+(PDB code: 1EI0).</h4>
+<div>
+ <fieldset class="majorpoints">
+ <legend class="majorpointslegend"
+ style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+
+ <div class="hiders" style="display:none" >
+<p>
+In this example the PDB code of the selected protein (1EI0) and the OPT-WTFSA-2
+force field are selected:
+<p>
+<img src="static/min_adv.png" style="border:2px solid blueviolet">
+
+After the minimization is accomplished, the UNRES model of 1EI0 protein
+with two disulfide bonds as read from the respective PDB file,
+its total UNRES energy and superposition on the starting structure are displayed:
+<p>
+<a href="static/min_adv1.png"><img src="static/min_adv1.png" width="300px"></a>
+<a href="static/min_adv2.png"><img src="static/min_adv2.png" width="300px"></a>
+<a href="static/min_adv3.png"><img src="static/min_adv3.png" width="300px"></a>
+
+ </div>
+</div>
+
+<h4><li>
+Canonical MD simulations of the Trp-Cage miniprotein (PDB code:1L2Y)
+starting from the extended chain.</h4>
+<div>
+ <fieldset class="majorpoints">
+ <legend class="majorpointslegend"
+ style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+
+ <div class="hiders" style="display:none" >
+In this example the PDB code of the selected protein (1L2Y) and
+option to write trajectory as a PDB file are selected, saving trajectory
+as a PDB file allows its 3D visualisation by NGL Viewer in addition to
+the movie which is always generated from the MD trajectory
+<p>
+<img src="static/md_adv.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/md_adv0.png" style="border:2px solid blueviolet">
+<p>
+After the MD simulation is accomplished temperature histogram,
+plots of UNRES energy, RMSD from the experimental structure, fraction of native
+contacts, and radius of gyration vs. time, and a movie of the trajectory are displayed.
+<p>
+<a href="static/md_adv1.png"><img src="static/md_adv1.png" width="300px"></a>
+<a href="static/md_adv2.png"><img src="static/md_adv2.png" width="300px"></a>
+<a href="static/md_adv3.png"><img src="static/md_adv3.png" width="300px"></a>
+<a href="static/md_adv4.png"><img src="static/md_adv4.png" width="300px"></a>
+<a href="static/md_adv5.png"><img src="static/md_adv5.png" width="300px"></a>
+<a href="static/md_adv6.png"><img src="static/md_adv6.png" width="300px"></a>
+<a href="static/md_adv7.png"><img src="static/md_adv7.png" width="300px"></a>
+<p>
+The CA fluctuations are not analyzed for start from the extended structure
+because of large scale conformational changes during folding.
+
+ </div>
+</div>
+
+
+<h4><li>
+MREMD simulations of 5G3Q:B (CASP12 target T0882)</h4>
+
+<div>
+ <fieldset class="majorpoints">
+ <legend class="majorpointslegend"
+ style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
+
+ <div class="hiders" style="display:none" >
+This simulation starts from the extended chain, 2000000 steps for each of 16
+replicas (8 temperatures with multiplexing 2)
+are run and secondary-structure restraints predicted by PSIPRED and
+obtained at the CASP12 time when the experimental 5G3Q structure
+was not included in the PDB database are used. The Berendsen thermostat
+was employed and the resulting conformational ensemble was clustered
+at the temperature of 290K.
+This is a full-blown structure-prediction run, but shorter
+compared to the UNRES runs during the CASP exercises.
+
+<p>
+<img src="static/remd_adv.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/remd_adv01.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/remd_adv02.png" style="border:2px solid blueviolet">
+<br>
+...
+<br>
+<img src="static/remd_adv03.png" style="border:2px solid blueviolet">
+<p>
+
+
+The output items are the same as those discussed with the Basic mode Example 3.
+<p>
+<a href="static/remd_adv1.png"><img src="static/remd_adv1.png" width="300px"></a>
+<a href="static/remd_adv2.png"><img src="static/remd_adv2.png" width="300px"></a>
+<a href="static/remd_adv3.png"><img src="static/remd_adv3.png" width="300px"></a>
+<a href="static/remd_adv6.png"><img src="static/remd_adv6.png" width="300px"></a>
+<a href="static/remd_adv7.png"><img src="static/remd_adv7.png" width="300px"></a>
+<a href="static/remd_adv8.png"><img src="static/remd_adv8.png" width="300px"></a>
+<a href="static/remd_adv4.png"><img src="static/remd_adv4.png" width="300px"></a>
+<a href="static/remd_adv5.png"><img src="static/remd_adv5.png" width="300px"></a>
+<p>
+The final models are shown using NGL Viewer.
+PDB files can be downloaded by clicking on the <i>Download</i> button.
+The RMSD of model 1
+from the experimental structure is 3.6 A and
+the GDT_TS is 58.8 %
+
+<p>
+<a href="static/remd_adv9.png"><img src="static/remd_adv9.png" width="300px"></a>
+
+<p>
+
+
+ </div>
+</div>
+
+