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<div class="section" id="simulation-of-a-protein">
<h1>Simulation of a protein<a class="headerlink" href="#simulation-of-a-protein" 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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73</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># A simple Molecular Dynamics simulation.</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">Amber99ForceField</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">Heater</span><span class="p">,</span> \
<span class="n">TranslationRemover</span><span class="p">,</span> <span class="n">RotationRemover</span>
<span class="kn">from</span> <span class="nn">MMTK.Visualization</span> <span class="kn">import</span> <span class="n">view</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">RestartTrajectoryOutput</span><span class="p">,</span> <span class="n">StandardLogOutput</span><span class="p">,</span> \
<span class="n">trajectoryInfo</span>
<span class="c"># Define system</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">InfiniteUniverse</span><span class="p">(</span><span class="n">Amber99ForceField</span><span class="p">(</span><span class="n">mod_files</span><span class="o">=</span><span class="p">[</span><span class="s">'frcmod.ff99SB'</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="p">(</span><span class="s">'bala1'</span><span class="p">)</span>
<span class="c"># Initialize velocities</span>
<span class="n">universe</span><span class="o">.</span><span class="n">initializeVelocitiesToTemperature</span><span class="p">(</span><span class="mf">50.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">K</span><span class="p">)</span>
<span class="k">print</span> <span class="s">'Temperature: '</span><span class="p">,</span> <span class="n">universe</span><span class="o">.</span><span class="n">temperature</span><span class="p">()</span>
<span class="k">print</span> <span class="s">'Momentum: '</span><span class="p">,</span> <span class="n">universe</span><span class="o">.</span><span class="n">momentum</span><span class="p">()</span>
<span class="k">print</span> <span class="s">'Angular momentum: '</span><span class="p">,</span> <span class="n">universe</span><span class="o">.</span><span class="n">angularMomentum</span><span class="p">()</span>
<span class="c"># Create integrator</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="c"># Heating and equilibration</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="c"># Heat from 50 K to 300 K applying a temperature</span>
<span class="c"># change of 0.5 K/fs; scale velocities at every step.</span>
<span class="n">actions</span><span class="o">=</span><span class="p">[</span><span class="n">Heater</span><span class="p">(</span><span class="mf">50.</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">K</span><span class="p">,</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="p">,</span> <span class="mf">0.5</span><span class="o">*</span><span class="n">Units</span><span class="o">.</span><span class="n">K</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="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span>
<span class="c"># Remove global translation every 50 steps.</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">50</span><span class="p">),</span>
<span class="c"># Remove global rotation every 50 steps.</span>
<span class="n">RotationRemover</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">50</span><span class="p">),</span>
<span class="c"># Log output to screen every 100 steps.</span>
<span class="n">StandardLogOutput</span><span class="p">(</span><span class="mi">100</span><span class="p">)])</span>
<span class="c"># "Production" run</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">"bala1.nc"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">,</span> <span class="s">"A simple test case"</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">100</span><span class="p">,</span>
<span class="c"># Remove global translation every 50 steps.</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">50</span><span class="p">),</span>
<span class="c"># Remove global rotation every 50 steps.</span>
<span class="n">RotationRemover</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">50</span><span class="p">),</span>
<span class="c"># Write every second step to the trajectory file.</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">"time"</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">"configuration"</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">2</span><span class="p">),</span>
<span class="c"># Write restart data every fifth step.</span>
<span class="n">RestartTrajectoryOutput</span><span class="p">(</span><span class="s">"restart.nc"</span><span class="p">,</span> <span class="mi">5</span><span class="p">),</span>
<span class="c"># Log output to screen every 10 steps.</span>
<span class="n">StandardLogOutput</span><span class="p">(</span><span class="mi">10</span><span class="p">)])</span>
<span class="n">trajectory</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="c"># Print information about the trajectory file</span>
<span class="k">print</span> <span class="s">"Information about the trajectory file 'bala1.nc':"</span>
<span class="k">print</span> <span class="n">trajectoryInfo</span><span class="p">(</span><span class="s">'bala1.nc'</span><span class="p">)</span>
<span class="c"># Reopen trajectory file</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">"bala1.nc"</span><span class="p">,</span> <span class="s">"r"</span><span class="p">)</span>
<span class="c"># Read step 10 and display configuration</span>
<span class="n">step10</span> <span class="o">=</span> <span class="n">trajectory</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span>
<span class="n">view</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">step10</span><span class="p">[</span><span class="s">'configuration'</span><span class="p">])</span>
<span class="c"># Print the kinetic energy along the trajectory</span>
<span class="k">print</span> <span class="s">"Kinetic energy along trajectory:"</span>
<span class="k">print</span> <span class="n">trajectory</span><span class="o">.</span><span class="n">kinetic_energy</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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