<div dir="ltr"><div class="gmail_default" style="color:#000000">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></div><div class="gmail_default" style="color:#000000"><br></div><div class="gmail_default" style="color:#000000">Mostafa
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</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Apr 7, 2020 at 5:20 PM Thomas Kühne <<a href="mailto:tku...@gmail.com">tku...@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Have you also adapted the coordinates, or simply modified the cell geometry? <div>If not you may first try to carefully prepare your initial state taken the presence </div><div>of periodic boundary conditions into account ...</div><div><br></div><div>Cheers, </div><div>Thomas<br><div><br><blockquote type="cite"><div>Am 07.04.2020 um 23:08 schrieb Mostafa Abedi <<a href="mailto:mostaf...@brown.edu" target="_blank">mostaf...@brown.edu</a>>:</div><br><div><div dir="ltr"><div>Dear Thomas,</div><div><br></div><div>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><br></div><div>Best,</div><div><br></div><div>Mostafa</div><div><br></div><div><br></div><div><br></div><div><br></div><br>On Tuesday, April 7, 2020 at 4:14:44 PM UTC-4, tkuehne wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;"><div>Dear Mostafa, </div><div><br></div>you are relying on the default values for the thermostat. For such a small system (the fluctuations scale with the sqrt <div>of the number of particles), a strong coupling is necessary. Try for instance REGION MASSIVE, TYPE CSVR and </div><div>TIMECON 50. More importantly, however, the dimension of your cell is too large resulting in a way too low density. </div><div><div><br></div><div>Cheers, </div><div>Thomas<br><div><div><br><blockquote type="cite"><div>Am 07.04.2020 um 21:51 schrieb Mostafa Abedi <<a rel="nofollow">abe...@gmail.com</a>>:</div><br><div><div dir="ltr"><div>Hi Everybody,</div><div><br></div><div>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><br></div><div>Best,</div><div>Mostafa </div></div><div><br></div>
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