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thermodynamics-integration-from-scratch-using-cp2k.html
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thermodynamics integration from scratch using cp2k
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<i class="fa fa-calendar"></i><time datetime="2014-11-20T12:52:00+01:00"> Thu 20 November 2014</time>
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<p>2 ions in 512 water system is using to calculation the Potential of Mean Force (PMF) for ion pair. ( I was using 64 water system where the size of the box is only about 12.0Å, the PMF can only exceed to 6.0Å, if I use 512 water system the box size can be more than 24Å the PMF can exceed to 10.0Å. )</p>
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<p>I need to know the size of the box with such number of water and ion in the system. (maybe not necessary for such big system, I put it here for smaller system and large concentration ionic solutions) Details are in my code.</p>
<p><a href="./codes/cal_density.py">cal_density.py</a></p>
<p><a href="./codes/cal_density_512h2o.py">cal_density_512h2o.py</a></p>
<p>The box size calculated for NaCl in 512H2O is 24.8736639347 Å.</p>
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<p>Generate the initial structure for my simulation. I use gromacs and vmd to do that.
First using genbox tool in gromacs to generate a box of water with 514 water in it. The size is a little bit larger to make sure enough water molecules can be included.</p>
<div class="highlight"><pre><span></span><code>genbox_d -cs spc216.gro -box 2.52 2.52 2.52 -maxsol 514
</code></pre></div>
<p>In this way, I got a out.gro file. I will rename it to h2o514.gro file. And edit it to change the last two water to a Na ion and a Cl ion. Also the size of the box will be changed as well as the index of the atoms and the total number of atoms in the top of the file. Then I rename it to h2o512NaCl.gro. I have the final version of it here.
<a href="./codes/h2o512NaCl.gro">h2o512NaCl.gro</a></p>
<p>I would like to use psf and xyz file for the input of topology information and coordinations in to cp2k. VMD is used here for this task. So I use the script I wrote for vmd.
<a href="./codes/tr_psf512.vmd">tr_psf512.vmd</a>
it used in this way.</p>
<div class="highlight"><pre><span></span><code>vmd -e tr_psf512.vmd
</code></pre></div>
<p>The files I got here is H2O512NaCl.xyz, and H2O512NaCl_gro.psf . They also need to be edited (OW -> O, HW1, HW2 -> H, the atom mass, and change the form of psf to upsf which can be loaded by cp2k). The final version of these two files are given here.
<a href="./codes/H2O512NaCl.xyz">H2O512NaCl.xyz</a>
<a href="./codes/H2O512NaCl_gro.psf">H2O512NaCl_gro.psf</a>
(This structure is not good enough for directly calculation since the cell size is not the same. I will try to use packmol to regenerate another initial structure for the calculation later.)</p>
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<p>The force field I am using is <a href="http://scitation.aip.org/content/aip/journal/jcp/130/12/10.1063/1.3081142">SPCE/HMN</a>. An online <a href="http://www.colby.edu/chemistry/PChem/Hartree.html">energy unit convertion tool</a> is used for the parameters.</p>
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<p>The <a href="./codes/H2O_SPCE_HMN.inp">input file</a> for cp2k. It is the input file for constraint dynamics. The lagrange multiplier will print out for the constraint force for the thermodynamics integration calculation. </p>
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