Thank you so much! that did the trick.<br><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Friday, May 13, 2022 at 12:03:40 AM UTC-5 Matthias Krack 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 lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div> <p class="MsoNormal"><span lang="EN-US">Hi Eric<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US">I suggest to increase the cutoff from 150 to 300 Ry and to decrease EPS_DEFAULT to 1.0E-12 and EPS_SCF to 1.0E-7. Use IOLEVEL medium and check if the accuracy of the electron count at the end of the first SCF iteration is at least 1.0E-7 (if it converges?). Check for warnings about close contacts. You can force a check for short interatomic distances with <a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/PRINT/INTERATOMIC_DISTANCES.html#CHECK_INTERATOMIC_DISTANCES" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/PRINT/INTERATOMIC_DISTANCES.html%23CHECK_INTERATOMIC_DISTANCES&source=gmail&ust=1652548886646000&usg=AOvVaw2UI3htgbdw9YTO3tJoM9VE"> this keyword</a> if your system has more than 2000 atoms. I suggest to perform an initial structure relaxation using the RUN_TYPE GEO_OPT.<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US">HTH<u></u><u></u></span></p> <p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p> <p class="MsoNormal"><span lang="EN-US">Matthias<u></u><u></u></span></p></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div> <p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-left:36.0pt"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">"<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>" <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>> on behalf of Eric Ledieu <<a href data-email-masked rel="nofollow">eric.ledi...@gmail.com</a>><br> <b>Reply to: </b>"<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>" <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>><br> <b>Date: </b>Thursday, 12 May 2022 at 20:29<br> <b>To: </b>"<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>" <<a href data-email-masked rel="nofollow">cp...@googlegroups.com</a>><br> <b>Subject: </b>[CP2K:16959] Re: hydrogen shooting out randomly<u></u><u></u></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> <p class="MsoNormal" style="margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> right, that is rather bare. I am running AIMD with the following script. <u></u><u></u></p> </div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div> <div> <p class="MsoNormal" style="margin-left:36.0pt">On Thursday, May 12, 2022 at 11:55:19 AM UTC-5 Marcella Iannuzzi wrote:<u></u><u></u></p> </div> </div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> <p class="MsoNormal" style="margin-left:36.0pt">Dear Eric <u></u><u></u></p> <div> <p class="MsoNormal" style="margin-left:36.0pt">the information you provide are not sufficient to understand what is going wrong in the simulation<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">cp2k can run MM with the amber force field<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Regards<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> Marcella<u></u><u></u></p> </div> </blockquote></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div> <div> <p class="MsoNormal" style="margin-left:36.0pt">On Thursday, May 12, 2022 at 6:10:26 PM UTC+2 <span><a href data-email-masked rel="nofollow">eric.ledi...@gmail.com</a></span> wrote:<u></u><u></u></p> </div> </div></blockquote></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <p class="MsoNormal" style="margin-left:36.0pt">Dear CP2K community<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">I am seeing some odd behavior with the hydrogen on a couple of molecules. I think it is something to do with periodic boundary interactions, and I was wondering if there was a way to minimize initial positions. I don't have classical MD parameters ready, as I am running it AIMD, but I can assign GAFF values and run it a round through amber minimization I guess, but I don't know if CP2K can take amber output. Any guidance would be much appreciated. <u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">With best wishes<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt">Eric<u></u><u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> </blockquote></div></blockquote></div></div></div><div lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><div><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"><p class="MsoNormal" style="margin-left:36.0pt"><img border="0" src="https://groups.google.com/group/cp2k/attach/5bf4fab969e3a/Screen%20Shot%202022-05-12%20at%2010.56.06%20AM.png?part=0.1&view=1"><u></u><u></u></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><u></u> <u></u></p> </div> </blockquote> </div> </blockquote> </div> <p class="MsoNormal" style="margin-left:36.0pt">-- <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">cp2k+uns...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/a84b943c-b43a-4fe5-88a1-06a434eebc1fn%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/a84b943c-b43a-4fe5-88a1-06a434eebc1fn%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1652548886647000&usg=AOvVaw3Uuqtcw8UgBQrnQedeZ9YS"> https://groups.google.com/d/msgid/cp2k/a84b943c-b43a-4fe5-88a1-06a434eebc1fn%40googlegroups.com</a>.<br> <br> <u></u><u></u></p> </div> </div> </blockquote></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+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/6b48b7f3-5d67-4383-a7ce-9bece70571d5n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/6b48b7f3-5d67-4383-a7ce-9bece70571d5n%40googlegroups.com</a>.<br />