amics)">
<h2>Initialize the system (A larger damping coefficient for the Brownian Dynamics)<a class="headerlink" href="#Initialize-the-system-(A-larger-damping-coefficient-for-the-Brownian-Dynamics)" title="Permalink to this headline">¶</a></h2>
<p>We first set up an example “model” of class “OpenNucleome” with the conserved temperature, damping coefficient, timestep, and the mass scale. In this folder, we also included the initial configuration “human.pdb” used for the simulation and created a