<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Guillaume, <div class=""><br class=""></div><div class="">as written in the paper only modified O-O & O-H parameter sets were </div><div class="">provided, i.e. the H-H interactions should be taken from the original mio </div><div class="">parameter set. To the best of my knowledge, the latter is indeed the </div><div class="">0-1 version. </div><div class=""><br class=""></div><div class="">Best, </div><div class="">Thomas</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">Am 28.12.2018 um 17:06 schrieb Guillaume Stirnemann <<a href="mailto:gsti...@gmail.com" class="">gsti...@gmail.com</a>>:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div dir="ltr" class="">Dear Thomas, <div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">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" class="">https://www.dftbplus.org/fileadmin/DFTBPLUS/public/dftbplus/latest/manual.pdf</a><span class="Apple-converted-space"> </span>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 class=""><br class=""></div><div class="">Thanks again! </div><div class=""><br class=""></div><div class="">Best </div><div class=""><br class=""></div><div class="">Guillaume </div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div></div></div><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class="gmail_quote" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div dir="ltr" class="">On Thu, Dec 27, 2018 at 2:48 PM Thomas Kühne <<a href="mailto:tku...@gmail.com" class="">tku...@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div style="overflow-wrap: break-word;" class="">Dear Guillaume, <div class=""><br class=""></div><div class="">I have a couple of (hopefully helpful) comments using DFTB within CP2K: </div><div class="">1. To the best of my knowledge only the mio and znorg parameter sets, </div><div class="">i.e. the ob2 parameter set needs to be downloaded from<span class="Apple-converted-space"> </span><a href="http://dftb.org/" target="_blank" class="">dftb.org</a></div><div class="">2. IMHO, the usage of a damped gamma does not represent a general </div><div class="">improvement, it marginally improves the 1st peak for water but appears </div><div class="">to be worse for a lot of other systems</div><div class="">3. I rather suggest to use the improved parametrization of Dömer et al., </div><div class="">see e.g. <a href="https://arxiv.org/pdf/1408.5161.pdf" target="_blank" class="">https://arxiv.org/pdf/1408.5161.pdf</a> and references therein. </div><div class="">Since I couldn’t find the files anywhere else, I have attached them to the </div><div class="">present email. We will check them again and upload them to the repository </div><div class="">next week. </div><div class="">4. For comparison have a look at Fig. 1-3 in<span class="Apple-converted-space"> </span><a href="https://arxiv.org/pdf/1512.08206.pdf" target="_blank" class="">https://arxiv.org/pdf/1512.08206.pdf</a> </div><div class="">for a plain DFTB calculation of liquid water by CP2K with the provided original </div><div class="">parametrization, without the modified gamma and no vdw correction, but including </div><div class="">nuclear quantum effects. No inhomogeneity in the particle density have been observed. </div><div class="">5. Please also have a look at the recent discussion about the SPME settings, </div><div class="">which may play a role in your observed behavior.</div><div class=""><br class=""></div><div class="">Best, </div><div class="">Thomas</div><div class=""><br class=""></div><div class=""></div></div><div class=""><br class="webkit-block-placeholder"></div>--<span class="Apple-converted-space"> </span><br class="">You received this message because you are subscribed to the Google Groups "cp2k" group.<br class="">To unsubscribe from this group and stop receiving emails from it, send an email to<span class="Apple-converted-space"> </span><a href="mailto:cp2k+uns...@googlegroups.com" target="_blank" class="">cp2k+uns...@googlegroups.com</a>.<br class="">To post to this group, send email to<span class="Apple-converted-space"> </span><a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a>.<br class="">Visit this group at<span class="Apple-converted-space"> </span><a href="https://groups.google.com/group/cp2k" target="_blank" class="">https://groups.google.com/group/cp2k</a>.<br class="">For more options, visit<span class="Apple-converted-space"> </span><a href="https://groups.google.com/d/optout" target="_blank" class="">https://groups.google.com/d/optout</a>.<br class=""><div style="overflow-wrap: break-word;" class=""><div class=""></div></div><div class=""><br class="webkit-block-placeholder"></div>--<span class="Apple-converted-space"> </span><br class="">You received this message because you are subscribed to the Google Groups "cp2k" group.<br class="">To unsubscribe from this group and stop receiving emails from it, send an email to<span class="Apple-converted-space"> </span><a href="mailto:cp2k+uns...@googlegroups.com" target="_blank" class="">cp2k+uns...@googlegroups.com</a>.<br class="">To post to this group, send email to<span class="Apple-converted-space"> </span><a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a>.<br class="">Visit this group at<span class="Apple-converted-space"> </span><a href="https://groups.google.com/group/cp2k" target="_blank" class="">https://groups.google.com/group/cp2k</a>.<br class="">For more options, visit<span class="Apple-converted-space"> </span><a href="https://groups.google.com/d/optout" target="_blank" class="">https://groups.google.com/d/optout</a>.<br class=""><div style="overflow-wrap: break-word;" class=""><div class=""></div></div><div class=""><br class="webkit-block-placeholder"></div>--<span class="Apple-converted-space"> </span><br class="">You received this message because you are subscribed to the Google Groups "cp2k" group.<br class="">To unsubscribe from this group and stop receiving emails from it, send an email to<span class="Apple-converted-space"> </span><a href="mailto:cp2k+uns...@googlegroups.com" target="_blank" class="">cp2k+uns...@googlegroups.com</a>.<br class="">To post to this group, send email to<span class="Apple-converted-space"> </span><a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a>.<br class="">Visit this group at<span class="Apple-converted-space"> </span><a href="https://groups.google.com/group/cp2k" target="_blank" class="">https://groups.google.com/group/cp2k</a>.<br class="">For more options, visit<span class="Apple-converted-space"> </span><a href="https://groups.google.com/d/optout" target="_blank" class="">https://groups.google.com/d/optout</a>.<br class=""><div style="overflow-wrap: break-word;" class=""><div class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">Am 26.12.2018 um 16:33 schrieb Guillaume Stirnemann <<a href="mailto:gsti...@gmail.com" target="_blank" class="">gsti...@gmail.com</a>>:</div><br class="gmail-m_1666502237632698503Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi all, <div class=""><br class=""></div><div class="">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 class="">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 class="">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 class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">Best wishes</div><div class=""><br class=""></div><div class="">Guillaume </div><div class="">CNRS Institut de Biologie Physico-Chimique, Paris, France</div></div>--<span class="Apple-converted-space"> </span><br class="">You received this message because you are subscribed to the Google Groups "cp2k" group.<br class="">To unsubscribe from this group and stop receiving emails from it, send an email to<span class="Apple-converted-space"> </span><a href="mailto:cp2k+uns...@googlegroups.com" target="_blank" class="">cp2k+uns...@googlegroups.com</a>.<br class="">To post to this group, send email to<span class="Apple-converted-space"> </span><a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a>.<br class="">Visit this group at<span class="Apple-converted-space"> </span><a href="https://groups.google.com/group/cp2k" target="_blank" class="">https://groups.google.com/group/cp2k</a>.<br class="">For more options, visit<span class="Apple-converted-space"> </span><a href="https://groups.google.com/d/optout" target="_blank" class="">https://groups.google.com/d/optout</a>.<br class=""><span id="gmail-m_1666502237632698503cid:bc358444-a670-487f-82e5-372264ecefa8" class=""><<a href="http://input-dftb2-gamma-nod.in/" target="_blank" class="">input-DFTB2-gamma-noD.in</a>></span><span id="gmail-m_1666502237632698503cid:751413f9-b298-478e-936a-8c391631e2e8" class=""><<a href="http://h2o.xyz/" target="_blank" class="">h2o.xyz</a>></span></div></blockquote><br class=""></div></div><div class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><span class="gmail-m_1666502237632698503Apple-style-span" style="border-collapse: separate; 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;" class=""><span class="gmail-m_1666502237632698503Apple-style-span" style="border-collapse: separate; 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;" class=""><span class="gmail-m_1666502237632698503Apple-style-span" style="border-collapse: separate; 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;" class=""><span style="text-align: -webkit-auto;" class="">==============================</span></div><div style="overflow-wrap: break-word;" class=""><div class=""><div style="overflow-wrap: break-word;" class=""><div style="overflow-wrap: break-word;" class=""><div style="overflow-wrap: break-word;" class=""><div style="overflow-wrap: break-word;" class=""><div style="overflow-wrap: break-word;" class=""><div class="">Prof. Dr. Thomas D. Kühne</div><div class="">Dynamics of Condensed Matter</div><div class="">Chair of Theoretical Chemistry</div><div class="">University of Paderborn</div><div class="">Warburger Str. 100</div><div class="">D-33098 Paderborn</div><div class="">Germany</div><div class=""><a href="mailto:tdku...@mail.upb.de" target="_blank" class="">tdku...@mail.upb.de</a></div><div class="">+49/(0)5251/60-5726</div></div></div></div></div></div></div></div></span></div></span></div></span></div></div></div></div><br class=""></div><div class=""><br class="webkit-block-placeholder"></div>--<span class="Apple-converted-space"> </span><br class="">You received this message because you are subscribed to the Google Groups "cp2k" group.<br class="">To unsubscribe from this group and stop receiving emails from it, send an email to<span class="Apple-converted-space"> </span><a href="mailto:cp2k+uns...@googlegroups.com" target="_blank" class="">cp2k+uns...@googlegroups.com</a>.<br class="">To post to this group, send email to<span class="Apple-converted-space"> </span><a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a>.<br class="">Visit this group at<span class="Apple-converted-space"> </span><a href="https://groups.google.com/group/cp2k" target="_blank" class="">https://groups.google.com/group/cp2k</a>.<br class="">For more options, visit<span class="Apple-converted-space"> </span><a href="https://groups.google.com/d/optout" target="_blank" class="">https://groups.google.com/d/optout</a>.<br class=""></blockquote></div><div style="font-family: Helvetica; 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