Dear Guillaume<br><br>Thank you very much for your reply and for sharing that information.<br>I will try to run the calculations with SCC-DFTB and the water parameters you mentioned.<br><br>Best regards<br>Pedro<br><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, July 8, 2021 at 4:25:11 PM UTC+1 gs...@gmail.com wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr"><div dir="ltr"><br></div>Dear Pedro, <div><br></div><div>Unfortunately, this is a known issue with tight-binding methods such as DFTB or xTB. It has been reported before, see e.g. <a href="https://pubs.acs.org/doi/abs/10.1021/jp400953a" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://pubs.acs.org/doi/abs/10.1021/jp400953a&source=gmail&ust=1625848428647000&usg=AFQjCNG3R12u5wZvA75c5mbppGtGX3d6ww">https://pubs.acs.org/doi/abs/10.1021/jp400953a</a>, although it does not seem to be widely communicated. This info had been nicely shared by Thomas Kühne and Juerg Hutter here some time ago (see Dec 2018). </div><div>Systems shrink unreasonably in the NPT ensemble, and usually, bubbles appear if the volume is kept constant to satisfy the experimental density. It is pretty clear by looking at the radial distribution functions that the structure is usually pretty badly reproduced. </div><div><br></div><div>In my group we did many many tests using different generations of TB methods in cp2k, including xTB. The only set of parameters that seem to give "stable" results for water (in the NVT ensemble) are the SCC-DFTB, sometimes called DFTB2, using the mio-1-1 parameter set. Thomas also shared some parameters that were reoptimized to better reproduce water structure, see in <a href="https://arxiv.org/pdf/1408.5161.pdf" rel="nofollow" style="text-decoration-line:none;color:rgb(26,115,232);font-family:Roboto,RobotoDraft,Helvetica,Arial,sans-serif;font-size:14px" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://arxiv.org/pdf/1408.5161.pdf&source=gmail&ust=1625848428648000&usg=AFQjCNG3oXhsTY7Gnwmpk9JE3EiWuh4oeQ">https://arxiv.org/pdf/1408.5161.pdf</a><font color="#a00029" face="Roboto, RobotoDraft, Helvetica, Arial, sans-serif"><span style="font-size:14px">. </span></font></div><div>These parameters do not lead to voids in the simulation box, but I never tested them in NPT. </div><div><br></div><div>It seems that later generations of xTB seem give much more accurate results in general (no idea how they behave for liquid water), but I don't think they are currently implemented in cp2k. </div><div><br></div><div>Best wishes, </div><div><br></div><div>Guillaume Stirnemann </div><div><br></div><div><br><div class="gmail_quote"></div></div></div><div dir="ltr"><div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 7, 2021 at 7:01 PM Pedro Maximiano <<a href data-email-masked rel="nofollow">pe...@gmail.com</a>> wrote:<br></div></div></div></div><div dir="ltr"><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear CP2K users and developers<br><br>I'm a relatively new CP2K user, and I'm trying to do MD simulations of a dimer of a small molecule in water with the GFN-xTB method. To prepare the simulations I first minimize and then equilibrate the boxes in a NPT ensemble (300 K, 1 bar) with the AMBER force field, followed by a short NVT run (also with AMBER FF). I then start the xTB simulation from the final point of the classical MD run, in the NVT ensemble (300 K). However, I noticed that voids appear in the xTB simulation boxes, probably indicative of a wrong system density.<br><br>To reproduce the issue in a simpler system, I ran a NPT simulation with xTB (300 K, 1 bar) on a box of 126 water molecules in CP2K. The box was pre-equilibrated in a NPT run (also 300 K, 1 bar), with the AMBER FF TIP3P parameters, yielding a density of 1.023 g/cm3. This box was then subjected to a minimization and a short NVT equilibration with xTB, prior to the NPT equilibration. Indeed, I observed that the xTB NPT run compressed the box, to a final density of 1.481 g/cm3.<br><br>I'm attaching here the input for the xTB NPT simulation of water. The sections that are commented are settings which I also tried, without success, namely:<br>- Adding a NONBONDED potential to xTB (taken from the test file xTB/regtest-debug/h2o-atprop_nonbonded.inp)<br><div>- Changing the settings in the POISSON/EWALD section to non default values (up to RCUT = 10.0 Angstrom)</div><div><br></div>Note that I also ran the test xTB/regtest-debug/h2o-atprop_nonbonded.inp for 20000 steps and obtained an abnormally high density (1.722 g/cm3).<br>All runs were performed in CP2K v8.2, but I also noticed the same issues when running in version 7.1.<br><br>Could you please take a look at the input file and tell me if I'm missing something?<br><br>Best regards<br>Pedro Maximiano <p></p></blockquote></div></div></div><div dir="ltr"><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/7e0dd338-885f-469f-acdd-2a32e8dda682n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://groups.google.com/d/msgid/cp2k/7e0dd338-885f-469f-acdd-2a32e8dda682n%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1625848428648000&usg=AFQjCNFSL8fo2OT0rUi3lxLiIiqTV5xIGQ">https://groups.google.com/d/msgid/cp2k/7e0dd338-885f-469f-acdd-2a32e8dda682n%40googlegroups.com</a>.<br> </blockquote></div></div></div> </blockquote></div>