                <span class="c1"># 0.1: damping coefficient (LJ reduced unit);</span>
                                           <span class="c1"># 0.005: timestep (LJ reduced unit);</span>
                                           <span class="c1"># 1.0: mass_scale</span>

<span class="n">PDB_file</span> <span class="o">=</span> <span class="s2">&quot;initial_configs/human_1.pdb&quot;</span>   <span class="c1">#The initial configuration</span>

<span class="c1"># Generate new elements and construct topolo