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generate initial structure by packmol
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<p>The initial structure for md simulation will be generated by packmol then do an equilibrium step by lammps. The system I would like to prepare is 4M NaCl solution. ( 9 Na+ 9 Cl- and 115 H2O with the box size 15.5473 A. ) The template structure of Na+ and Cl- and tip4p H2O structure are prepared first. </p>
<p>na.xyz</p>
<div class="highlight"><pre><span></span><code><span class="mf">2</span>
<span class="n">Na</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">NaD</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.02</span>
</code></pre></div>
<p>cl.xyz</p>
<div class="highlight"><pre><span></span><code><span class="mf">2</span>
<span class="n">Cl</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">ClD</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.02</span>
</code></pre></div>
<p>tip4p.xyz</p>
<div class="highlight"><pre><span></span><code><span class="mf">3</span>
<span class="n">O</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">H</span> <span class="o">-</span><span class="mf">0.75695</span> <span class="mf">0.58588</span> <span class="mf">0.0</span>
<span class="n">H</span> <span class="mf">0.75695</span> <span class="mf">0.58588</span> <span class="mf">0.0</span>
</code></pre></div>
<p>and also I have the input file for packmol with the name of packmol_NaClH2O.inp</p>
<div class="highlight"><pre><span></span><code>#
# <span class="nv">A</span> <span class="nv">mixture</span> <span class="nv">of</span> <span class="nv">water</span> <span class="nv">and</span> <span class="nv">NaCl</span>
#
<span class="nv">tolerance</span> <span class="mi">2</span>.<span class="mi">5</span>
<span class="nv">filetype</span> <span class="nv">xyz</span>
<span class="nv">output</span> <span class="nv">NaClH2O</span>.<span class="nv">xyz</span>
<span class="nv">structure</span> <span class="nv">tip4p</span>.<span class="nv">xyz</span>
<span class="nv">number</span> <span class="mi">115</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">15</span>.<span class="mi">0473</span> <span class="mi">15</span>.<span class="mi">0473</span> <span class="mi">15</span>.<span class="mi">0473</span> # <span class="mi">15</span>.<span class="mi">5473</span>
<span class="k">end</span> <span class="nv">structure</span>
<span class="nv">structure</span> <span class="nv">na</span>.<span class="nv">xyz</span>
<span class="nv">number</span> <span class="mi">9</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">15</span>.<span class="mi">0473</span> <span class="mi">15</span>.<span class="mi">0473</span> <span class="mi">15</span>.<span class="mi">0473</span> # <span class="mi">15</span>.<span class="mi">5473</span>
<span class="k">end</span> <span class="nv">structure</span>
<span class="nv">structure</span> <span class="nv">cl</span>.<span class="nv">xyz</span>
<span class="nv">number</span> <span class="mi">9</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">15</span>.<span class="mi">0473</span> <span class="mi">15</span>.<span class="mi">0473</span> <span class="mi">15</span>.<span class="mi">0473</span> # <span class="mi">15</span>.<span class="mi">5473</span>
<span class="k">end</span> <span class="nv">structure</span>
</code></pre></div>
<p>Then run packmol.sh script</p>
<div class="highlight"><pre><span></span><code>PACKMOL="$HOME/software/packmol/packmol/packmol"
INPUT=packmol_NaClH2O.inp
$PACKMOL < $INPUT
</code></pre></div>
<p>With the help of vmd program, the data file and psf topo file are generated.</p>
<div class="highlight"><pre><span></span><code><span class="x">mol new NaClH2O.xyz waitfor all</span>
<span class="x">pbc set </span><span class="cp">{</span> <span class="m">15.5473</span> <span class="m">15.5473</span> <span class="m">15.5473</span> <span class="cp">}</span><span class="x"></span>
<span class="x">#add bonds and angles</span>
<span class="x">topo clearbonds</span>
<span class="x">for </span><span class="cp">{</span><span class="nf">set</span> <span class="na">i</span> <span class="m">0</span><span class="cp">}</span><span class="x"> </span><span class="cp">{</span><span class="nv">$i</span> <span class="o"><</span> <span class="m">115</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">$i</span><span class="o">*</span><span class="m">3</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">+</span><span class="m">1</span><span class="o">]</span> <span class="o">-</span><span class="na">bondtype</span> <span class="m">1</span> <span class="err">#</span><span class="na">bond</span> <span class="na">O</span><span class="o">-</span><span class="na">H</span>
<span class="na">topo</span> <span class="na">addbond</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">+</span><span class="m">2</span><span class="o">]</span> <span class="o">-</span><span class="na">bondtype</span> <span class="m">1</span> <span class="err">#</span><span class="na">bond</span> <span class="na">O</span><span class="o">-</span><span class="na">H</span>
<span class="na">topo</span> <span class="na">addangle</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">+</span><span class="m">2</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="nv">$i</span><span class="o">*</span><span class="m">3</span><span class="o">+</span><span class="m">1</span><span class="o">]</span> <span class="m">1</span> <span class="err">#</span><span class="na">angle</span> <span class="na">H</span><span class="o">-</span><span class="na">O</span><span class="o">-</span><span class="na">H</span>
<span class="cp">}</span><span class="x"></span>
<span class="x">for </span><span class="cp">{</span><span class="nf">set</span> <span class="na">i</span> <span class="m">0</span><span class="cp">}</span><span class="x"> </span><span class="cp">{</span><span class="nv">$i</span> <span class="o"><</span> <span class="m">18</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="m">115</span><span class="o">*</span><span class="m">3</span><span class="o">+</span><span class="nv">$i</span><span class="o">*</span><span class="m">2</span><span class="o">]</span> <span class="o">[</span><span class="na">expr</span> <span class="m">115</span><span class="o">*</span><span class="m">3</span><span class="o">+</span><span class="m">1</span><span class="o">+</span><span class="nv">$i</span><span class="o">*</span><span class="m">2</span><span class="o">]</span> <span class="o">-</span><span class="na">bondtype</span> <span class="m">2</span>
<span class="cp">}</span><span class="x"></span>
<span class="x">topo writelammpsdata data.NaClH2O</span>
<span class="x">animate write psf NaClH2O.psf</span>
</code></pre></div>
<p>Then I manually modified the molecule ids in data file.</p>
<p>After that, lammps is used to equilibrium the system.</p>
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