<div dir="ltr"><div dir="ltr">Hi Travis,<div><br></div><div>Thanks for complete explanation. Currently I am using NVE for MD part in my system. I tried to use NPT but it doesn't work for my system. So I prefer to stick to NVE as it goes to the right direction. I am still struggling with water molecules moving out of the simulation box. I have enclosed my input file and final coordinates.</div><div>Would you please have a look and give me some advises to fix this problem?</div><div><br></div><div>Many thanks in advance</div><div>Farzaneh</div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Oct 8, 2019 at 5:22 PM Travis <<a href="mailto:polla...@gmail.com" target="_blank">polla...@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi,</div><div><br></div><div>Compile the code with your preferred Fortran compiler,<br></div><div><div style="background-color:rgb(250,250,250);border:1px solid rgb(187,187,187)"><code><div><span style="color:rgb(0,0,0)">gfortran dumpdcd</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">f90</span></div></code></div></div><div><br></div><div>Run code on a host of DCD files you want to merge, these would be coming from a long simulation that you broke up into smaller segments,<br></div><span style="color:rgb(0,0,0)"></span><div><div style="background-color:rgb(250,250,250);border:1px solid rgb(187,187,187)"><code><div><span style="color:rgb(102,102,0)">./</span><span style="color:rgb(0,0,0)">a</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,136)">out</span><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(102,102,0)">-</span><span style="color:rgb(0,0,0)">xyz reference</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">xyz </span><span style="color:rgb(102,102,0)">-</span><span style="color:rgb(0,0,0)">pbc </span><span style="color:rgb(102,102,0)">-</span><span style="color:rgb(0,0,0)">of dcd </span><span style="color:rgb(102,102,0)">-</span><span style="color:rgb(0,0,0)">o full_foo_trajectory</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">dcd foo1</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">dcd foo2</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">dcd foo3</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">dcd </span><span style="color:rgb(102,102,0)">...</span><span style="color:rgb(0,0,0)"> fooN</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">dcd<br></span></div></code></div></div><div><br></div><div>You need a reference XYZ format file for determining atom name as DCD only contains lattice parameters and coordinates. The -pbc flag says to produce a wrapped trajectory, while leaving it off produces the unwrapped trajectory.<br><br>To wrap an XYZ trajectory requires TRAVIS (<a href="https://www.travis-analyzer.de/" target="_blank">https://www.travis-analyzer.de/</a>). In one of the advanced options, you can read the second line for each frame of the XYZ file as the lattice parameters in Angstroms and degrees. I give a more detailed explanation of it here, <a href="https://groups.google.com/forum/#!topic/cp2k/GNLdTcUZFUo" target="_blank">https://groups.google.com/forum/#!topic/cp2k/GNLdTcUZFUo</a> (for NPT). Alternatively, if you are comfortable with Python, you can use the Atomic Simulation Environment.</div><div><br></div><div>-T<br></div><br>On Tuesday, October 8, 2019 at 4:23:27 AM UTC-3, farzaneh sarrami wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr">Thanks Travis,<div><br></div><div>Would you please explain in more details how can I use dumpdcd.f90 script in cp2k ? as I have same problem.</div><div><br></div><div>Best,</div><div>Farzaneh</div><br>On Monday, October 7, 2019 at 5:01:01 PM UTC+2, Travis wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi,</div><div><br></div><div>CP2K dumps unwrapped coordinates, so they are not imaged back into the box if they drift beyond. A simple way to get a wrapped trajectory is to dump DCD files during MD, then use the dumpdcd.f90 script in tools/ to dump a wrapped DCD (-pbc option). I don't recommend writing XYZ format trajectories for MD. Write DCD and convert. Way easier to strip info than to add it back in.<br></div><div><br></div><div>-T</div><div><br></div><br>On Monday, October 7, 2019 at 8:09:09 AM UTC-3, Harender Singh wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Dear all, <br></div><div>I am running AIMD simulation of some electrolyte at Li electrode. While the electrolyte molecules are staying within the simulation cell, the electrode atoms are moving out of the cell. <br></div><div>Is there any possible explanation for that?</div><div>Is there something wrong with my simulation setup? If yes, then how can I correct it?</div><div><br></div><div>Thanks for the help in advance. <br></div></div></blockquote></div></blockquote></div></blockquote></div>
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