<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=""><div class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">Am 26.12.2018 um 16:33 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" 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>
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<span id="cid:bc358444-a670-487f-82e5-372264ecefa8"><<a href="http://input-DFTB2-gamma-noD.in" class="">input-DFTB2-gamma-noD.in</a>></span><span id="cid:751413f9-b298-478e-936a-8c391631e2e8"><h2o.xyz></span></div></blockquote><br class=""></div></div><div class="">
<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; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span class="Apple-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-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span class="Apple-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-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span class="Apple-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-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span style="text-align: -webkit-auto;" class="">==============================</span></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div apple-content-edited="true" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: 2; widows: 2;" class="">Prof. Dr. Thomas D. Kühne</div><div style="orphans: 2; widows: 2;" class="">Dynamics of Condensed Matter</div><div style="orphans: 2; widows: 2;" class="">Chair of Theoretical Chemistry</div><div style="orphans: 2; widows: 2;" class="">University of Paderborn</div><div style="orphans: 2; widows: 2;" class="">Warburger Str. 100</div><div style="orphans: 2; widows: 2;" class="">D-33098 Paderborn</div><div style="orphans: 2; widows: 2;" class="">Germany</div><div style="orphans: 2; widows: 2;" class=""><a href="mailto:tdku...@mail.upb.de" class="">tdku...@mail.upb.de</a></div><div style="orphans: 2; widows: 2;" class="">+49/(0)5251/60-5726</div></div></div></div></div></div></div></div></span></div></span></div></span></div></div></div>
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