<div dir="ltr"><div>Thank you Matt!</div><div><br></div><div>Best wishes,</div><div>Dawid<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2018-06-26 12:07 GMT+02:00 Matt W <span dir="ltr"><<a href="mailto:mattwa...@gmail.com" target="_blank">mattwa...@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">CP2K does not wrap molecules back into the box when writing an MD trajectory - so you can see the 'diffusion' of a molecule. This can be useful for analysis.<div><br></div><div>Whether you expect molecules to diffuse that far depends on the system / length of simulation time. You could try running a small box of water with classical MD and see how that looks.<br><div><br></div><div>As you note the molecule _is_ wrapped back into the cell when all calculations are done. You can safely wrap back into the cell for visualization etc.</div><span class="HOEnZb"><font color="#888888"><div><br></div></font></span><div><span class="HOEnZb"><font color="#888888">Matt</font></span><div><div class="h5"><br><br>On Tuesday, June 26, 2018 at 10:58:22 AM UTC+1, Dawid das wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi, <br></div><div><br></div><div>I would like to repeat my question, please.</div><div><br></div><div>Best wishes,</div><div>Dawid Grabarek<br></div><br>W dniu poniedziałek, 18 czerwca 2018 10:00:14 UTC+2 użytkownik Dawid das napisał:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Dear CP2K Users,</div><div><br></div><div>I am doing QM/MM MD simulation using PBC only for MM part (the QM cell is not periodic). My cell is <br></div><div>orthorombic and I am a bit surprised as in course of simulation some water molecules drift away to vacuum <br></div><div>when I use VMD to visualize my trajectory.</div><div><br></div><div>Now, I am aware that if PBC work it does not matter as the image of this molecule "enters on the other side"</div><div>however this visualization makes me to ask a question whether I do my setup correctly.</div><div><br></div><div>So in course of MD what I get in XYZ trajectory file is not wrapped by CP2K and can I safely wrap those <br></div><div>molecules/atoms later on with a script? In other words, does CP2K save only coordinates of molecules <br></div><div>found in starting geometry but not its images as they leave the box?</div><div><br></div><div>Best wishes,</div><div>Dawid</div><div><br></div><div>PS This is part of my input that should simply apply PBC, am I right?</div><div><br></div><div> &MM</div><div> &POISSON<br> PERIODIC XYZ<br> POISSON_SOLVER PERIODIC<br> &EWALD<br> EWALD_TYPE SPME<br>!3.5/12 Angstrom<br> ALPHA .292<br> GMAX 32 32 16<br> EWALD_ACCURACY 1.0E-6<br> &END EWALD<br> &END POISSON<br></div><div> &END MM</div><div><br></div><div> &SUBSYS<br> &CELL<br> ABC [nm] 7.60236 6.53052 6.03591<br> ALPHA_BETA_GAMMA 90 90 90<br> PERIODIC XYZ<br>! SYMMETRY ORTHORHOMBIC<br> &END CELL<br><br></div></div></blockquote></div></blockquote></div></div></div></div></div><div class="HOEnZb"><div class="h5">
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