s="n">chr_positions</span><span class="p">)</span>

<span class="n">simulation</span><span class="o">.</span><span class="n">minimizeEnergy</span><span class="p">()</span>

<span class="n">simulation</span><span class="o">.</span><span class="n">reporters</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mdtraj</span><span class="o">.</span><span class="n">reporters</span><span class="o">.</span><span class="n">DCDReporter</span><span class="p">(</span><span 