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dissipative particle dynamics
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<i class="fa fa-calendar"></i><time datetime="2014-11-22T23:27:00+01:00"> Sat 22 November 2014</time>
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<p>I learned about dissipative particle dynamics (DPD) with Max, Upendra, and Ardeshir. It is an amazing tool for simulation of mesoscale systems including polymers and bio-membranes.
The system size can be extened to µm ,and µs for time scale which is about 10^6 faster than regular molecular dynamics.</p>
<p>This post is for my learning process and materials of DPD.</p>
<p>Rob Groot seems to be the bigest name in the field of DPD. And he has really good slides for DPD. Here is the <a href="http://www.cecam.org/upload/talk/presentation_2751.pdf">link</a>. </p>
<p>In the presentation, he answered the question of how to parameterise DPD. The goal of it is to reproduce local thermodynamics which are measured by compressibility and solubility. Flory-Huggins theory are used for the solubility.</p>
<p>I tried to run dpd in lammps. With the input below.</p>
<div class="highlight"><pre><span></span><code><span class="p">#</span> <span class="n">This</span> <span class="n">is</span> <span class="n">LAMMPS</span> <span class="k">input</span> <span class="n">script</span> <span class="n">specifies</span> <span class="n">a</span> <span class="n">simple</span> <span class="n">DPD</span> <span class="n">simulation</span><span class="p">.</span>
<span class="p">#</span> <span class="n">It</span> <span class="n">reproduces</span> <span class="n">Fig</span><span class="p">.</span> <span class="mh">2</span> <span class="n">of</span> <span class="n">Groot</span> <span class="k">and</span> <span class="n">Warren</span><span class="p">,</span> <span class="n">J</span><span class="p">.</span> <span class="n">Chem</span><span class="p">.</span> <span class="n">Phys</span><span class="p">.</span> <span class="mh">107</span><span class="p">,</span>
<span class="p">#</span> <span class="mh">4423</span> <span class="p">(</span><span class="mh">1997</span><span class="p">)</span>
<span class="n">units</span> <span class="n">lj</span>
<span class="n">atom_style</span> <span class="n">atomic</span>
<span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
<span class="n">pair_style</span> <span class="n">dpd</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mh">34387</span>
<span class="p">#</span> <span class="n">create</span> <span class="n">simulation</span> <span class="n">box</span>
<span class="n">lattice</span> <span class="n">fcc</span> <span class="mh">3</span>
<span class="n">region</span> <span class="n">mybox</span> <span class="n">block</span> <span class="o">-</span><span class="mh">4</span> <span class="mh">4</span> <span class="o">-</span><span class="mh">4</span> <span class="mh">4</span> <span class="o">-</span><span class="mh">4</span> <span class="mh">4</span> <span class="n">units</span> <span class="n">lattice</span>
<span class="n">create_box</span> <span class="mh">1</span> <span class="n">mybox</span>
<span class="n">create_atoms</span> <span class="mh">1</span> <span class="n">box</span>
<span class="p">#</span> <span class="n">define</span> <span class="n">masses</span> <span class="k">and</span> <span class="n">interaction</span> <span class="n">coefficient</span>
<span class="n">mass</span> <span class="o">*</span> <span class="mh">1</span>
<span class="n">pair_coeff</span> <span class="mh">1</span> <span class="mh">1</span> <span class="mh">25</span> <span class="mf">4.5</span>
<span class="p">#</span> <span class="n">create</span> <span class="k">initial</span> <span class="n">velocities</span>
<span class="n">velocity</span> <span class="n">all</span> <span class="n">create</span> <span class="mf">1.0</span> <span class="mh">4928459</span> <span class="n">dist</span> <span class="n">gaussian</span>
<span class="p">#</span> <span class="n">change</span> <span class="n">neighbor</span> <span class="n">list</span> <span class="n">parameters</span> <span class="n">to</span> <span class="n">avoid</span> <span class="n">dangerous</span> <span class="n">builds</span>
<span class="n">neighbor</span> <span class="mf">2.0</span> <span class="n">bin</span>
<span class="n">neigh_modify</span> <span class="n">delay</span> <span class="mh">3</span>
<span class="p">#</span> <span class="k">specify</span> <span class="n">simulation</span> <span class="n">parameters</span>
<span class="n">timestep</span> <span class="mf">0.04</span>
<span class="n">thermo</span> <span class="mh">10</span>
<span class="p">#</span> <span class="n">first</span> <span class="n">equilibrate</span> <span class="n">the</span> <span class="k">initial</span> <span class="n">condition</span>
<span class="n">fix</span> <span class="mh">1</span> <span class="n">all</span> <span class="n">nve</span>
<span class="n">run</span> <span class="mh">500</span>
<span class="n">dump</span> <span class="n">traj</span> <span class="n">all</span> <span class="n">xtc</span> <span class="mh">50</span> <span class="n">traj</span><span class="p">.</span><span class="n">xtc</span>
<span class="n">dump_modify</span> <span class="n">traj</span> <span class="n">unwrap</span> <span class="n">yes</span>
<span class="n">dump</span> <span class="n">traj_xyz</span> <span class="n">all</span> <span class="n">xyz</span> <span class="mh">50</span> <span class="n">traj</span><span class="p">.</span><span class="n">xyz</span>
<span class="p">#</span> <span class="n">production</span> <span class="n">run</span>
<span class="n">run</span> <span class="mh">50000</span>
</code></pre></div>
<p>The gr plot I got from this simulation is the same as the plot 2 in the paper.</p>
<p><img alt="Alt Text" src="./images/gr_dpd.png"></p>
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