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<div class="section" id="solvation-of-a-protein-in-water">
<h1>Solvation of a protein in water<a class="headerlink" href="#solvation-of-a-protein-in-water" title="Permalink to this headline">ΒΆ</a></h1>
<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
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95</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># Solvation of a protein with water.</span>
<span class="c">#</span>
<span class="c"># The solvation procedure consists of three steps:</span>
<span class="c">#</span>
<span class="c"># - The universe containing the protein is scaled up, and the required</span>
<span class="c"># number of water molecules is added at random positions, but without</span>
<span class="c"># any overlap between molecules. The system is so dilute that random</span>
<span class="c"># placements are easily possible.</span>
<span class="c">#</span>
<span class="c"># - The universe is slowly scaled down do its original size, with</span>
<span class="c"># each scaling step followed by some energy minimization and</span>
<span class="c"># molecular dynamics steps.</span>
<span class="c">#</span>
<span class="c"># - A molecular dynamics run at constant pressure and temperature is</span>
<span class="c"># used to put the system into a well-defined thermodynamic state.</span>
<span class="c">#</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">MMTK.Proteins</span> <span class="kn">import</span> <span class="n">Protein</span>
<span class="kn">from</span> <span class="nn">MMTK.ForceFields</span> <span class="kn">import</span> <span class="n">Amber94ForceField</span>
<span class="kn">from</span> <span class="nn">MMTK.Environment</span> <span class="kn">import</span> <span class="n">NoseThermostat</span><span class="p">,</span> <span class="n">AndersenBarostat</span>
<span class="kn">from</span> <span class="nn">MMTK.Trajectory</span> <span class="kn">import</span> <span class="n">Trajectory</span><span class="p">,</span> <span class="n">TrajectoryOutput</span><span class="p">,</span> <span class="n">LogOutput</span>
<span class="kn">from</span> <span class="nn">MMTK.Dynamics</span> <span class="kn">import</span> <span class="n">VelocityVerletIntegrator</span><span class="p">,</span> <span class="n">VelocityScaler</span><span class="p">,</span> \
<span class="n">BarostatReset</span><span class="p">,</span> <span class="n">TranslationRemover</span>
<span class="kn">import</span> <span class="nn">MMTK.Solvation</span>
<span class="c"># Create the solute.</span>
<span class="n">protein</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="s">'bala1'</span><span class="p">)</span>
<span class="c"># Put the solvent in a standard configuration: center of mass at the</span>
<span class="c"># coordinate origin, principal axes of inertia parallel to the coordinate axes.</span>
<span class="n">protein</span><span class="o">.</span><span class="n">normalizeConfiguration</span><span class="p">()</span>
<span class="c"># Define density, pressure, and temperature of the solvent.</span>
<span class="n">water_density</span> <span class="o">=</span> <span class="mf">1.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">g</span><span class="o">/</span><span class="n">Units</span><span class="o">.</span><span class="n">cm</span><span class="o">**</span><span class="mi">3</span>
<span class="n">temperature</span> <span class="o">=</span> <span class="mf">300.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">K</span>
<span class="n">pressure</span> <span class="o">=</span> <span class="mf">1.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">atm</span>
<span class="c"># Calculate the box size as the boundary box of the protein plus an</span>
<span class="c"># offset. Note: a much larger offset should be used in real applications.</span>
<span class="n">box</span> <span class="o">=</span> <span class="n">protein</span><span class="o">.</span><span class="n">boundingBox</span><span class="p">()</span>
<span class="n">box</span> <span class="o">=</span> <span class="n">box</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">-</span><span class="n">box</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span>
<span class="c"># Create a periodic universe. The force field is intentionally created with</span>
<span class="c"># a rather small cutoff to speed up the solvation process.</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">OrthorhombicPeriodicUniverse</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">box</span><span class="p">),</span>
<span class="n">Amber94ForceField</span><span class="p">(</span><span class="mf">1.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">))</span>
<span class="n">universe</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="n">protein</span>
<span class="c"># Find the number of solvent molecules.</span>
<span class="k">print</span> <span class="n">MMTK</span><span class="o">.</span><span class="n">Solvation</span><span class="o">.</span><span class="n">numberOfSolventMolecules</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span><span class="s">'water'</span><span class="p">,</span><span class="n">water_density</span><span class="p">),</span>\
<span class="s">"water molecules will be added"</span>
<span class="c"># Scale up the universe and add the solvent molecules.</span>
<span class="n">MMTK</span><span class="o">.</span><span class="n">Solvation</span><span class="o">.</span><span class="n">addSolvent</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="s">'water'</span><span class="p">,</span> <span class="n">water_density</span><span class="p">)</span>
<span class="k">print</span> <span class="s">"Solvent molecules have been added, now shrinking universe..."</span>
<span class="c"># Shrink the universe back to its original size, thereby compressing</span>
<span class="c"># the solvent to its real density.</span>
<span class="n">MMTK</span><span class="o">.</span><span class="n">Solvation</span><span class="o">.</span><span class="n">shrinkUniverse</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">temperature</span><span class="p">,</span> <span class="s">'solvation.nc'</span><span class="p">)</span>
<span class="k">print</span> <span class="s">"Universe has been compressed, now equilibrating..."</span>
<span class="c"># Set a better force field and add thermostat and barostat.</span>
<span class="c">#</span>
<span class="c"># Note: For efficiency, optimized Ewald parameters should be used</span>
<span class="c"># in a real application. The barostat relaxation time must be</span>
<span class="c"># adjusted to the system size; it should be chosen smaller than</span>
<span class="c"># for a realistic simulation in order to reach the final</span>
<span class="c"># volume faster.</span>
<span class="n">universe</span><span class="o">.</span><span class="n">setForceField</span><span class="p">(</span><span class="n">Amber94ForceField</span><span class="p">(</span><span class="mf">1.4</span><span class="p">,</span> <span class="p">{</span><span class="s">'method'</span><span class="p">:</span> <span class="s">'ewald'</span><span class="p">}))</span>
<span class="n">universe</span><span class="o">.</span><span class="n">thermostat</span> <span class="o">=</span> <span class="n">NoseThermostat</span><span class="p">(</span><span class="n">temperature</span><span class="p">)</span>
<span class="n">universe</span><span class="o">.</span><span class="n">barostat</span> <span class="o">=</span> <span class="n">AndersenBarostat</span><span class="p">(</span><span class="n">pressure</span><span class="p">,</span> <span class="mf">0.1</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">ps</span><span class="p">)</span>
<span class="c"># Create an integrator and a trajectory.</span>
<span class="n">integrator</span> <span class="o">=</span> <span class="n">VelocityVerletIntegrator</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">delta_t</span><span class="o">=</span><span class="mf">1.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">fs</span><span class="p">)</span>
<span class="n">trajectory</span> <span class="o">=</span> <span class="n">Trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="s">"equilibration.nc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">,</span>
<span class="s">"Equilibration (NPT ensemble)"</span><span class="p">)</span>
<span class="c"># Start an NPT integration with periodic rescaling of velocities</span>
<span class="c"># and resetting of the barostat. The number of steps required to</span>
<span class="c"># reach a stable volume depends strongly on the system!</span>
<span class="n">output_actions</span> <span class="o">=</span> <span class="p">[</span><span class="n">TrajectoryOutput</span><span class="p">(</span><span class="n">trajectory</span><span class="p">,</span>
<span class="p">(</span><span class="s">'configuration'</span><span class="p">,</span> <span class="s">'energy'</span><span class="p">,</span> <span class="s">'thermodynamic'</span><span class="p">,</span>
<span class="s">'time'</span><span class="p">,</span> <span class="s">'auxiliary'</span><span class="p">),</span> <span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">100</span><span class="p">),</span>
<span class="n">LogOutput</span><span class="p">(</span><span class="s">"equilibration.log"</span><span class="p">,</span> <span class="p">(</span><span class="s">'time'</span><span class="p">,</span> <span class="s">'energy'</span><span class="p">),</span>
<span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">100</span><span class="p">)]</span>
<span class="n">integrator</span><span class="p">(</span><span class="n">steps</span> <span class="o">=</span> <span class="mi">1000</span><span class="p">,</span>
<span class="n">actions</span> <span class="o">=</span> <span class="p">[</span><span class="n">TranslationRemover</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">200</span><span class="p">),</span>
<span class="n">BarostatReset</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">20</span><span class="p">),</span>
<span class="n">VelocityScaler</span><span class="p">(</span><span class="n">temperature</span><span class="p">,</span> <span class="mf">0.</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">20</span><span class="p">)]</span>
<span class="o">+</span> <span class="n">output_actions</span><span class="p">)</span>
<span class="c"># Close the equilibration trajectory</span>
<span class="n">trajectory</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
</pre></div>
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