{% extends "base.html" %}

{% load i18n lazysignup_tags %}
{% block content %}

<h4>
In order to submit a job you need to provide its name:</h4>
<p>
<img src="static/name.png" style="border:2px solid blueviolet">

UNRES server allows three types of simulations: 
local minimization, molecular dynamics, replica exchange molecular dynamics:
<p>
<img src="static/types.png" style="border:2px solid blueviolet">
<p>
Use "Save & submit" button to start calculations.
<p>
Use "Refresh" button to check the status of simulation:
<p>
<img src="static/refresh.png" style="border:2px solid blueviolet">
<p>
until
<img src="static/done.png" style="border:2px solid blueviolet">
<p>


<h4>Use "Load example data" button before submitting calculations 
to try all examples listed below:</h4>
<p>
<ol>
<h4><li>Local minimization of protein A (PDB code:1BDD) structure</h4>
<div>
    <fieldset class="majorpoints">
        <legend class="majorpointslegend"
            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
    
    <div class="hiders" style="display:none" >
<p>
<img src="static/min.png" style="border:2px solid blueviolet">


The results of local minimizations show the UNRES model, its total energy 
and overlap on starting structure:
<p>
<a href="static/min1.png"><img src="static/min1.png" width="300px"></a>
<a href="static/min2.png"><img src="static/min2.png" width="300px"></a>
</div>
</div>

<hr>
<h4><li>Molecular dynamics of IGG-binding domain from streptococcal protein G
(PDB code:1IGD) starting from the native structure</h4>
<div>
    <fieldset class="majorpoints">
        <legend class="majorpointslegend"
            style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
    
    <div class="hiders" style="display:none" >

<p>
<img src="static/md.png" style="border:2px solid blueviolet">
<p>
The results of md simulations show temperature histogram, 
potential energy changes, evolution of radius of gyration,
RMSD, fraction of native contacts, and CA fluctuations:
<p>
<a href="static/md1.png"><img src="static/md1.png" width="300px"></a>
<a href="static/md2.png"><img src="static/md2.png" width="300px"></a>
<a href="static/md3.png"><img src="static/md3.png" width="300px"></a>
<a href="static/md4.png"><img src="static/md4.png" width="300px"></a>
<a href="static/md5.png"><img src="static/md5.png" width="300px"></a>
<a href="static/md6.png"><img src="static/md6.png" width="300px"></a>
<a href="static/md7.png"><img src="static/md7.png" width="300px"></a>
<a href="static/md8.png"><img src="static/md8.png" width="300px"></a>
<p>
Evolution of RMSD, fraction of native contacts and 
comparison of CA fluctuations to Bfactor is presented
only when reference structure is provided as in this case.
</div>
</div>
<hr>
<h4><li>
Replica exchange molecular dynamics of 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" >
<img src="static/remd.png" style="border:2px solid blueviolet">
<p>

Plots of histograms of UNRES energy for each temperature, and
energy vs temperature are presented.
The weighted histogram analysis (WHAM) is applied to compute the
probabilities of the obtained conformations to occur at particular
temperatures, plots of heat capacity and average RMSD as a functions
of temperature are shown. Replica exchanges are analyzed.
<p>
<a href="static/remd1.png"><img src="static/remd1.png" width="300px"></a>
<a href="static/remd2.png"><img src="static/remd2.png" width="300px"></a>
<a href="static/remd3.png"><img src="static/remd3.png" width="300px"></a>
<a href="static/remd4.png"><img src="static/remd4.png" width="300px"></a>
<a href="static/remd5.png"><img src="static/remd5.png" width="300px"></a>
<a href="static/remd6.png"><img src="static/remd6.png" width="300px"></a>
<a href="static/remd7.png"><img src="static/remd7.png" width="300px"></a>
<a href="static/remd8.png"><img src="static/remd8.png" width="300px"></a>
<p>
Finally cluster analysis is performed to select 5 families of conformations,
and representative model from each family is converted to all-atom
and refined. 
<p>
<a href="static/remd9.png"><img src="static/remd9.png" width="300px"></a>

<p>


</div>
</div>
<hr>
Advanced mode allows for changes of more parameters of each type of
simulation. Separate examples are provided: minimization of 1EI0 with
dissulfide bonds, MD simulations of 1L2Y starting from extended chain
and replica exchange simulations of 1E0G starting form extended chain 
using new UNRES force field and Berendsen thermostat.

<script src="/static/jquery.min.js"></script>

<script>
$('.majorpoints').click(function(){
    $(this).find('.hiders').toggle();
    if($(this).find('.majorpointslegend').text()=='Show'){
        $(this).find('.majorpointslegend').text('Hide');
    }else{
        $(this).find('.majorpointslegend').text('Show');
    }    
});
</script>


{% endblock %}