<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I was told that Packmol is very helpful: <a href="http://m3g.iqm.unicamp.br/packmol/home.shtml" class="">http://m3g.iqm.unicamp.br/packmol/home.shtml</a>. <div class="">Also, at tests/QS/benchmark (or regtests in general) you will find equilibrated water </div><div class="">configurations for all sort of system sizes starting from 32 molecules. </div><div class=""><br class=""></div><div class="">Greetings, </div><div class="">Thomas<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">Am 08.04.2020 um 20:37 schrieb Mostafa Abedi <<a href="mailto:mostaf...@brown.edu" class="">mostaf...@brown.edu</a>>:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div style="" class="">You are right, I just changed the unit cell
in the input file to the one that fits the structure. Is there any
program/visualizer for preparing the initial state that takes the
presence of periodic boundary conditions into account? <br class=""></div><div style="" class=""><br class=""></div><div class="">Mostafa <br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><br class="">On Tuesday, April 7, 2020 at 5:20:12 PM UTC-4, tkuehne wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div style="word-wrap:break-word;line-break:after-white-space" class="">Have you also adapted the coordinates, or simply modified the cell geometry? <div class="">If not you may first try to carefully prepare your initial state taken the presence </div><div class="">of periodic boundary conditions into account ...</div><div class=""><br class=""></div><div class="">Cheers, </div><div class="">Thomas<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">Am 07.04.2020 um 23:08 schrieb Mostafa Abedi <<a target="_blank" gdf-obfuscated-mailto="Ak-Q-k4nBAAJ" rel="nofollow" class="">mos...@brown.edu</a>>:</div><br class=""><div class=""><div dir="ltr" class=""><div class="">Dear Thomas,</div><div class=""><br class=""></div><div class="">Many thanks for your help. I've changed the input file according to your suggestion. However, the temperature fluctuation is getting larger. I attached the corresponding files. I really appropriate if you could have another look into this. Thanks.</div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class="">Mostafa</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><br class="">On Tuesday, April 7, 2020 at 4:14:44 PM UTC-4, tkuehne wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space" class=""><div class="">Dear Mostafa, </div><div class=""><br class=""></div>you are relying on the default values for the thermostat. For such a small system (the fluctuations scale with the sqrt <div class="">of the number of particles), a strong coupling is necessary. Try for instance REGION MASSIVE, TYPE CSVR and </div><div class="">TIMECON 50. More importantly, however, the dimension of your cell is too large resulting in a way too low density. </div><div class=""><div class=""><br class=""></div><div class="">Cheers, </div><div class="">Thomas<br class=""><div class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">Am 07.04.2020 um 21:51 schrieb Mostafa Abedi <<a rel="nofollow" class="">abe...@gmail.com</a>>:</div><br class=""><div class=""><div dir="ltr" class=""><div class="">Hi Everybody,</div><div class=""><br class=""></div><div class="">I am trying to do NVT AIMD simulations for a system consisting of 16 H2O molecule. Strangely, the temperature fluctuation is very large (see attached "WATER-1.ener" file). I know a little bit temperature fluctuation is acceptable, but mine is really large. This is the first time I am trying CP2K for doing AIMD and not familiar with structure of the input file. Maybe something is wrong or missing in the input file (see attached "water.inp" file). I should say I've already done this calculation with ORCA for non-periodic water system. Now, I want to see the effect of periodicity with cp2k. Any help would greatly appropriated. Many thanks.</div><div class=""><br class=""></div><div class="">Best,</div><div class="">Mostafa </div></div><div class=""><br class=""></div>
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