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dissipative particle dynamics of membrane from scratch
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<i class="fa fa-calendar"></i><time datetime="2014-11-25T13:44:00+01:00"> Tue 25 November 2014</time>
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<p>I perform a test dpd simulation of membrane started from the generation of structures. packmol is used for generate the input structure. lammps is used as the simulator. </p>
<p>The lipid structure is as follow(lipid.xyz):</p>
<div class="highlight"><pre><span></span><code><span class="mf">11</span>
<span class="n">C</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">C</span> <span class="mf">0.5</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">C</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">C</span> <span class="mf">1.5</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">C</span> <span class="mf">0.0</span> <span class="mf">0.6</span> <span class="mf">0.0</span>
<span class="n">C</span> <span class="mf">0.5</span> <span class="mf">0.6</span> <span class="mf">0.0</span>
<span class="n">C</span> <span class="mf">1.0</span> <span class="mf">0.6</span> <span class="mf">0.0</span>
<span class="n">C</span> <span class="mf">1.5</span> <span class="mf">0.6</span> <span class="mf">0.0</span>
<span class="n">H</span> <span class="mf">2.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">H</span> <span class="mf">2.0</span> <span class="mf">0.5</span> <span class="mf">0.0</span>
<span class="n">H</span> <span class="mf">2.5</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
</code></pre></div>
<p>which is like the pic shown below.</p>
<p><img alt="Alt Text" src="./images/lipid.png"></p>
<p>also a water sturcture is listed(water.xyz). Because only one particle will represent one water.</p>
<div class="highlight"><pre><span></span><code><span class="mf">1</span>
<span class="n">W</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
</code></pre></div>
<p>a packmol input(bilayer_packmol.in) script is used here to generate the structure of the total system.</p>
<div class="highlight"><pre><span></span><code><span class="nv">tolerance</span> <span class="mi">0</span>.<span class="mi">5</span>
<span class="nv">filetype</span> <span class="nv">xyz</span>
<span class="nv">output</span> <span class="nv">bilayer</span>.<span class="nv">xyz</span>
<span class="nv">structure</span> <span class="nv">lipid</span>.<span class="nv">xyz</span>
<span class="nv">number</span> <span class="mi">250</span>
<span class="nv">inside</span> <span class="nv">box</span> <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">10</span>. <span class="mi">19</span>.<span class="mi">428</span> <span class="mi">19</span>.<span class="mi">428</span> <span class="mi">13</span>.<span class="mi">0</span>
<span class="nv">atoms</span> <span class="mi">1</span>
<span class="nv">below</span> <span class="nv">plane</span> <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">1</span>. <span class="mi">10</span>.<span class="mi">5</span>
<span class="k">end</span> <span class="nv">atoms</span>
<span class="nv">atoms</span> <span class="mi">11</span>
<span class="nv">over</span> <span class="nv">plane</span> <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">1</span>. <span class="mi">12</span>.<span class="mi">5</span>
<span class="k">end</span> <span class="nv">atoms</span>
<span class="k">end</span> <span class="nv">structure</span>
<span class="nv">structure</span> <span class="nv">lipid</span>.<span class="nv">xyz</span>
<span class="nv">number</span> <span class="mi">250</span>
<span class="nv">inside</span> <span class="nv">box</span> <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">7</span>.<span class="mi">0</span> <span class="mi">19</span>.<span class="mi">428</span> <span class="mi">19</span>.<span class="mi">428</span> <span class="mi">10</span>.<span class="mi">0</span>
<span class="nv">atoms</span> <span class="mi">1</span> <span class="mi">5</span>
<span class="nv">over</span> <span class="nv">plane</span> <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">1</span>. <span class="mi">9</span>.<span class="mi">5</span>
<span class="k">end</span> <span class="nv">atoms</span>
<span class="nv">atoms</span> <span class="mi">11</span>
<span class="nv">below</span> <span class="nv">plane</span> <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">1</span>. <span class="mi">7</span>.<span class="mi">5</span>
<span class="k">end</span> <span class="nv">atoms</span>
<span class="k">end</span> <span class="nv">structure</span>
<span class="nv">structure</span> <span class="nv">water</span>.<span class="nv">xyz</span>
<span class="nv">number</span> <span class="mi">8250</span>
<span class="nv">inside</span> <span class="nv">box</span> <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">12</span>.<span class="mi">5</span> <span class="mi">19</span>.<span class="mi">428</span> <span class="mi">19</span>.<span class="mi">428</span> <span class="mi">19</span>.<span class="mi">428</span>
<span class="k">end</span> <span class="nv">structure</span>
<span class="nv">structure</span> <span class="nv">water</span>.<span class="nv">xyz</span>
<span class="nv">number</span> <span class="mi">8250</span>
<span class="nv">inside</span> <span class="nv">box</span> <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">0</span>. <span class="mi">19</span>.<span class="mi">428</span> <span class="mi">19</span>.<span class="mi">428</span> <span class="mi">7</span>.<span class="mi">5</span>
<span class="k">end</span> <span class="nv">structure</span>
</code></pre></div>
<p>And also I have a script for the generation of psf and lammps data file.</p>
<div class="highlight"><pre><span></span><code><span class="x">mol new bilayer.xyz</span>
<span class="x">pbc set </span><span class="cp">{</span> <span class="m">19.428</span> <span class="m">19.428</span> <span class="m">19.428</span> <span class="cp">}</span><span class="x"></span>
<span class="x">topo clearbonds</span>
<span class="x">for </span><span class="cp">{</span><span class="nf">set</span> <span class="na">i</span> <span class="m">0</span><span class="cp">}</span><span class="x"> </span><span class="cp">{</span><span class="nv">$i</span> <span class="o"><</span> <span class="m">500</span><span class="cp">}</span><span class="x"> </span><span class="cp">{</span><span class="nf">incr</span> <span class="na">i</span><span class="cp">}</span><span class="x"> </span><span class="cp">{</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">1</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">1</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">2</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">2</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">3</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">4</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">5</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">5</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">6</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">6</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">7</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">3</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">8</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">7</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">9</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">8</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">9</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">8</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">10</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addangle</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">1</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">2</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addangle</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">1</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">2</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">3</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addangle</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">2</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">3</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">8</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addangle</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">4</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">5</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">6</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addangle</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">5</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">6</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">7</span><span class="o">]</span>
<span class="na">topo</span> <span class="na">addangle</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">6</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">7</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">11</span><span class="o">+</span><span class="m">9</span><span class="o">]</span>
<span class="cp">}</span><span class="x"></span>
<span class="x">animate write psf bilayer.psf</span>
<span class="x">topo writelammpsdata bilayer.data</span>
</code></pre></div>
<p>The final version of the input structure is showed as follow</p>
<p><img alt="Alt Text" src="./images/membrane.png"></p>
<p>I use this structure for the input of DPD simulation, and the input file for lammps is as follow. </p>
<p>The input files: <a href="./codes/bilayer.data">bilayer.data</a>, <a href="./codes/dpd_test.in">dpd_test.in</a></p>
<div class="highlight"><pre><span></span><code><span class="n">units</span> <span class="n">lj</span>
<span class="n">atom_style</span> <span class="n">full</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="n">read_data</span> <span class="n">bilayer</span><span class="p">.</span><span class="n">data</span>
<span class="p">#</span> <span class="n">create</span> <span class="n">simulation</span> <span class="n">box</span>
<span class="p">#</span><span class="n">lattice</span> <span class="n">fcc</span> <span class="mh">3</span>
<span class="p">#</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="p">#</span><span class="n">create_box</span> <span class="mh">1</span> <span class="n">mybox</span>
<span class="p">#</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="p">#</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">10</span> <span class="mf">4.5</span>
<span class="n">pair_coeff</span> <span class="mh">2</span> <span class="mh">2</span> <span class="mh">30</span> <span class="mf">4.5</span>
<span class="n">pair_coeff</span> <span class="mh">3</span> <span class="mh">3</span> <span class="mh">25</span> <span class="mf">4.5</span>
<span class="n">pair_coeff</span> <span class="mh">1</span> <span class="mh">2</span> <span class="mh">35</span> <span class="mf">4.5</span>
<span class="n">pair_coeff</span> <span class="mh">1</span> <span class="mh">3</span> <span class="mh">75</span> <span class="mf">4.5</span>
<span class="n">pair_coeff</span> <span class="mh">2</span> <span class="mh">3</span> <span class="mh">30</span> <span class="mf">4.5</span>
<span class="n">bond_style</span> <span class="n">harmonic</span>
<span class="n">bond_coeff</span> <span class="mh">1</span> <span class="mf">128.0</span> <span class="mf">0.5</span>
<span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span>
<span class="n">angle_coeff</span> <span class="mh">1</span> <span class="mf">7.5</span> <span class="mf">180.0</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 result movie is shown as below</p>
<p><img alt="Alt Text" src="./images/dpd_movie.gif"></p>
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