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<div class="section" id="restarting-the-protein-simulation">
<h1>Restarting the protein simulation<a class="headerlink" href="#restarting-the-protein-simulation" 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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54</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># Continuation of the simulation from protein.py using the restart</span>
<span class="c"># trajectory.</span>
<span class="c">#</span>
<span class="c"># Note: Restart trajectories don't differ much from ordinary</span>
<span class="c"># trajectories; they have a fixed number of steps that are reused</span>
<span class="c"># cyclically, but otherwise they are plain trajectory files.</span>
<span class="c"># As a consequence, you can restart a molecular dynamics run</span>
<span class="c"># from any trajectory that contains positions and velocities,</span>
<span class="c"># with only a minor modification mentioned below.</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.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">Amber94ForceField</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 system state from the restart trajectory</span>
<span class="n">universe</span><span class="o">.</span><span class="n">setFromTrajectory</span><span class="p">(</span><span class="n">Trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="s">"restart.nc"</span><span class="p">))</span>
<span class="c"># Note: for restarting from a standard trajectory, use:</span>
<span class="c">#</span>
<span class="c"># universe.setFromTrajectory(Trajectory(universe, "trajectory.nc"), -1)</span>
<span class="c">#</span>
<span class="c"># in order to load the last step (default would be the first one).</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"># Do some more MD steps.</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">"a"</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>
</pre></div>
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