<div dir="ltr"><div dir="ltr">Dear Thomas, <div><br></div><div>Thanks a lot for your comments. I ran quick tests following some of your suggestions and I think I have figured out where the problem might come from. It seems to be related with the use of damped gamma. I tried a short simulation (20 ps) without the gamma scaling on and using the standard cp2k parameters for SCC-DFTB, and everything seems fine. Now, this is very strange because this did not seem to cause any problems when used in DFTB+ (JPCB 115, 6790 (2011)). Has anyone some experience with the use of damped gamma in cp2k?</div><div><br></div><div>Thanks for pointing out some recent optimizations of the DFTB2 parameters (by the way, in the files you sent the hh spl file seems to be missing, right?). However, I would eventually need to perform simulations on molecules containing atoms other than C, N, O or H, so I may have to stick with a less-accurate set of parameters. Some more related questions below: </div><div><br></div><div>1) From what I understand, the spl files provided with cp2k corresponds to the mio 0-1 parameter set. Is this right? Some parameters (e.g. for phosphorus) seem to differ from the current mio 1-1 version. </div><div><br></div><div>2) For the molecules I am interested in, DFTB3-diag would probably be more suitable. But the problem is that it was parametrized with the damped gamma for hydrogens, for which there is the issue discussed above. </div><div><br></div><div>3) I would like to try to include the D3 corrections for dispersion interactions. The only thing which is not clear to me is the values I have to specify for D3_SCALING. Should I follow the values mentioned for the zero-damping case in the DFTB+ manual (see <a href="https://www.dftbplus.org/fileadmin/DFTBPLUS/public/dftbplus/latest/manual.pdf">https://www.dftbplus.org/fileadmin/DFTBPLUS/public/dftbplus/latest/manual.pdf</a> p45)? However, they seem to correspond to full DFTB3, whereas cp2k only has SCC-DFTB and DFTB3-diag. If anyone has experience regarding which D3_SCALING to use in that case, this would be great. </div><div><br></div><div>Thanks again! </div><div><br></div><div>Best </div><div><br></div><div>Guillaume </div><div><br></div><div><br></div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Dec 27, 2018 at 2:48 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;">Dear Guillaume, <div><br></div><div>I have a couple of (hopefully helpful) comments using DFTB within CP2K: </div><div>1. To the best of my knowledge only the mio and znorg parameter sets, </div><div>i.e. the ob2 parameter set needs to be downloaded from <a href="http://dftb.org" target="_blank">dftb.org</a></div><div>2. IMHO, the usage of a damped gamma does not represent a general </div><div>improvement, it marginally improves the 1st peak for water but appears </div><div>to be worse for a lot of other systems</div><div>3. I rather suggest to use the improved parametrization of Dömer et al., </div><div>see e.g. <a href="https://arxiv.org/pdf/1408.5161.pdf" target="_blank">https://arxiv.org/pdf/1408.5161.pdf</a> and references therein. </div><div>Since I couldn’t find the files anywhere else, I have attached them to the </div><div>present email. We will check them again and upload them to the repository </div><div>next week. </div><div>4. For comparison have a look at Fig. 1-3 in <a href="https://arxiv.org/pdf/1512.08206.pdf" target="_blank">https://arxiv.org/pdf/1512.08206.pdf</a> </div><div>for a plain DFTB calculation of liquid water by CP2K with the provided original </div><div>parametrization, without the modified gamma and no vdw correction, but including </div><div>nuclear quantum effects. No inhomogeneity in the particle density have been observed. </div><div>5. Please also have a look at the recent discussion about the SPME settings, </div><div>which may play a role in your observed behavior.</div><div><br></div><div>Best, </div><div>Thomas</div><div><br></div><div></div></div> <p></p> -- <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="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank">https://groups.google.com/group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br> <div style="overflow-wrap: break-word;"><div></div></div> <p></p> -- <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="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank">https://groups.google.com/group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br> <div style="overflow-wrap: break-word;"><div></div></div> <p></p> -- <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="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank">https://groups.google.com/group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br> <div style="overflow-wrap: break-word;"><div></div><div><br><div><blockquote type="cite"><div>Am 26.12.2018 um 16:33 schrieb Guillaume Stirnemann <<a href="mailto:gsti...@gmail.com" target="_blank">gsti...@gmail.com</a>>:</div><br class="gmail-m_1666502237632698503Apple-interchange-newline"><div><div dir="ltr">Hi all, <div><br></div><div>I am trying to simulate a box of liquid water using DFTB with periodic boundary conditions. My initial configuration is taken from a previous classical MD run performed in the NVT ensemble at the experimental density. </div><div>I have tried different set-ups, including SCC-DFTB ("DFTB2") and DFTB3-diag, both with or without Grimme's D3 corrections, all ran in the NVT ensemble for 50 ps. </div><div>In all cases, the simulations run well, but I end-up with a large hole in the simulation box. When comparing my radial distribution functions that of Cui who used DFBT+ (JPCB 115, 6790 (2011)), the first peak of the O-H rdf is usually a bit more pronounced but the contraction of the whole system is more visible on the second hydration shell. The differences are less visible for the O-O rdfs. The hole occupies about 1/2 of the simulation box, so the final density of my liquid phase is about 2! </div><div><br></div><div>I attach the initial configuration, and the cp2k input file for DFTB2 with no D3. I tried on two different machines, one with 6.1 and the other one with 5.1. </div><div><br></div><div>I am not an expert of CP2K so there might be some issues with my input, and your help would be very much appreciated. </div><div><br></div><div>Best wishes</div><div><br></div><div>Guillaume </div><div>CNRS Institut de Biologie Physico-Chimique, Paris, France</div></div> -- <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="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank">https://groups.google.com/group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br> <span id="gmail-m_1666502237632698503cid:bc358444-a670-487f-82e5-372264ecefa8"><<a href="http://input-DFTB2-gamma-noD.in" target="_blank">input-DFTB2-gamma-noD.in</a>></span><span id="gmail-m_1666502237632698503cid:751413f9-b298-478e-936a-8c391631e2e8"><<a href="http://h2o.xyz" target="_blank">h2o.xyz</a>></span></div></blockquote><br></div></div><div> <div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span class="gmail-m_1666502237632698503Apple-style-span" style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px"><div style="overflow-wrap: break-word;"><span class="gmail-m_1666502237632698503Apple-style-span" style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px"><div style="overflow-wrap: break-word;"><span class="gmail-m_1666502237632698503Apple-style-span" style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;border-spacing:0px"><div style="overflow-wrap: break-word;"><span style="text-align:-webkit-auto">==============================</span></div><div style="overflow-wrap: break-word;"><div><div style="overflow-wrap: break-word;"><div style="overflow-wrap: break-word;"><div style="overflow-wrap: break-word;"><div style="overflow-wrap: break-word;"><div style="overflow-wrap: break-word;"><div>Prof. Dr. Thomas D. Kühne</div><div>Dynamics of Condensed Matter</div><div>Chair of Theoretical Chemistry</div><div>University of Paderborn</div><div>Warburger Str. 100</div><div>D-33098 Paderborn</div><div>Germany</div><div><a href="mailto:tdku...@mail.upb.de" target="_blank">tdku...@mail.upb.de</a></div><div>+49/(0)5251/60-5726</div></div></div></div></div></div></div></div></span></div></span></div></span></div></div></div> </div> <br></div> <p></p> -- <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="mailto:cp2k+uns...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> Visit this group at <a href="https://groups.google.com/group/cp2k" target="_blank">https://groups.google.com/group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br> </blockquote></div>