<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Bence Baranyi, <br class=""><div class=""><br class=""></div><div class="">I do this either directly inside my own post-processing analysis tools, or via the PBCTools </div><div class="">plug-in within VMD: <a href="https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/" class="">https://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/</a></div><div class=""><div><br class=""></div><div>Best, Thomas Kühne</div><div><br class=""><blockquote type="cite" class=""><div class="">Am 03.01.2022 um 18:17 schrieb Bence Baranyi <<a href="mailto:babuteck@gmail.com" class="">babuteck@gmail.com</a>>:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Thomas Kühne,</div><div class=""><br class=""></div>thank you for your answer! Is there a way to fold the molecules back after the simulations? I need them to be in the original box since the box was chosen for a specific density of ammonia. I know, for example, GROMACS has an easy way to do this, but I don't know how to make this happen in CP2K.<br class=""><br class=""><div class="">Best regards,</div><div class="">Bence Baranyi</div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, December 16, 2021 at 11:08:17 AM UTC+1 tkuehne wrote:<br class=""></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div style="word-wrap:break-word;line-break:after-white-space" class="">Dear Bence Baranyi, <div class=""><br class=""></div><div class="">the coordinates in the output file are not folded back into the simulation box. </div><div class="">CP2K intern, however, periodic boundary conditions are strictly enforced, so </div><div class="">your „molecules stay in the initially given cell“. </div><div class=""><br class=""></div><div class="">Best, </div><div class="">Thomas Kühne</div><div class=""><div class=""><br class=""><blockquote type="cite" class=""></blockquote></div></div></div><div style="word-wrap:break-word;line-break:after-white-space" class=""><div class=""><div class=""><blockquote type="cite" class=""><div class="">Am 16.12.2021 um 11:01 schrieb Bence Baranyi <<a href="" data-email-masked="" rel="nofollow" class="">babu...@gmail.com</a>>:</div><br class=""></blockquote></div></div></div><div style="word-wrap:break-word;line-break:after-white-space" class=""><div class=""><div class=""><blockquote type="cite" class=""><div class=""><div class="">Hi!</div><div class="">I would like to make a simulation in CP2K, using AM1 on a system containing 33 NH3 molecules, in a cell with 10.855 angstroms as side length and with periodic boundary condition. My aim with this simulation is to get from randomly generated molecule positions to a somewhat realistic arrangement to be used later in an AIMD simulation. How can I ensure that the molecules stay in the said cell during the simulation? I attached the last structure of the simulation (and my input file) and as you can see the max distance between two molecules is clearly bigger than what it could be in a box with 10.855 angstrom sides.</div><div class="">All help is appreciated!</div><div class=""><br class=""></div></div></blockquote></div></div></div><div style="word-wrap:break-word;line-break:after-white-space" class=""><div class=""><div class=""><blockquote type="cite" class=""><div class="">
-- <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 <a href="" data-email-masked="" rel="nofollow" class="">cp2k+uns...@googlegroups.com</a>.<br class="">
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/130dff75-85a6-444c-afb2-c28618598be8n%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/130dff75-85a6-444c-afb2-c28618598be8n%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1641309906464000&usg=AFQjCNEqiDtMRNicR52QfbrdV5_fxNuSFw" class="">https://groups.google.com/d/msgid/cp2k/130dff75-85a6-444c-afb2-c28618598be8n%40googlegroups.com</a>.<br class="">
<span class=""><cp2k_am1_33nh3_last.txt></span><span class=""><bulk_33nh3.inp></span></div></blockquote></div></div><br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word; line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word; line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word; line-break: after-white-space;" class=""><div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word; line-break: after-white-space;" class=""><div style="font-family: Helvetica; font-size: 12px; 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: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">==============================</div><div style="font-family: Helvetica; font-size: 12px; 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: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Thomas D. Kühne</div><div style="font-family: Helvetica; font-size: 12px; 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: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Dynamics of Condensed Matter</div><div style="font-family: Helvetica; font-size: 12px; 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: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Chair of Theoretical Chemistry</div><div style="font-family: Helvetica; font-size: 12px; 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: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">University of Paderborn</div><div style="font-family: Helvetica; font-size: 12px; 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: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Warburger Str. 100</div><div style="font-family: Helvetica; font-size: 12px; 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: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">D-33098 Paderborn</div><div style="font-family: Helvetica; font-size: 12px; 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: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">Germany</div><div style="font-family: Helvetica; font-size: 12px; 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: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><a href="" data-email-masked="" rel="nofollow" class="">thomas...@upb.de</a></div><div style="font-family: Helvetica; font-size: 12px; 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: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class=""><a href="tel:+49%205251%20605726" value="+495251605726" target="_blank" rel="nofollow" class="">+49/(0)5251/60-5726</a></div></div></div></div></div>
</div>
<br class=""></div></blockquote></div><div class=""><br class="webkit-block-placeholder"></div>
-- <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 <a href="mailto:cp2k+unsubscribe@googlegroups.com" class="">cp2k+unsubscribe@googlegroups.com</a>.<br class="">
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/31644e8f-0b14-4b4b-9759-d7c69f058749n%40googlegroups.com?utm_medium=email&utm_source=footer" class="">https://groups.google.com/d/msgid/cp2k/31644e8f-0b14-4b4b-9759-d7c69f058749n%40googlegroups.com</a>.<br class="">
</div></blockquote></div><br class=""></div><br class=""><br class=""><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; 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; 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; 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; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">==============================</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Thomas D. Kühne</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Dynamics of Condensed Matter</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Chair of Theoretical Chemistry</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">University of Paderborn</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Warburger Str. 100</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">D-33098 Paderborn</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">Germany</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class=""><a href="mailto:thomas.kuehne@upb.de" class="">thomas.kuehne@upb.de</a></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class="">+49/(0)5251/60-5726</div></div></div></div></div>
</div>
<br class=""></body></html>
<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+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br />
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/F3DA7606-F0CA-4458-9D2D-552D5CC0FF14%40gmail.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/F3DA7606-F0CA-4458-9D2D-552D5CC0FF14%40gmail.com</a>.<br />