<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div class="WordSection1"> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US">Dear Léon<o:p></o:p></span></p> <p class="MsoNormal"><span lang="DE-CH" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">To avoid future confusion, I have added &FORCEFIELD sections for common 3-site water models to the <a href="https://github.com/cp2k/cp2k/tree/master/data/forcefield_section/H2O">cp2k database</a> (see cp2k/data/forcefield_section/H2O) and the corresponding <a href="https://github.com/cp2k/cp2k/tree/master/tests/Fist/regtest-water">template files</a> for 6x6x6 = 216 H2O water boxes are available as new regression tests. These template files can easily be modified (just adapt the @SET parameter na, nb, and nc lines in the top of each file) to generate arbitrary orthorhombic water boxes which can be equilibrated quickly.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Best<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <div id="mail-editor-reference-message-container"> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Léon Luntadila Lufungula <Leon.luntadilalufungula@uantwerpen.be><br> <b>Date: </b>Tuesday, 16 January 2024 at 09:14<br> <b>To: </b>cp2k <cp2k@googlegroups.com><br> <b>Subject: </b>Re: [CP2K:19756] Correct TIP3P parameters<o:p></o:p></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Dear Matthias,<o:p></o:p></span></p> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Thanks for clarifying this for me, I'll keep it in mind in the future when setting up my forcefield parameters.<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Kind regards,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <span style="font-size:11.0pt">Léon<o:p></o:p></span></p> </div> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">On Saturday 13 January 2024 at 10:18:21 UTC+1 Krack Matthias wrote:<o:p></o:p></span></p> </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="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Dear Léon</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">I have to correct my statement concerning the regression test inputs. The &BEND and &BOND section parameters in these inputs (e.g. in Fist/regtest-4/H2O-1.inp) are correct for the flexible TIP3P model, because the default value for the <a href="https://manual.cp2k.org/cp2k-2024_1-branch/CP2K_INPUT/FORCE_EVAL/MM/FORCEFIELD/BEND.html#CP2K_INPUT.FORCE_EVAL.MM.FORCEFIELD.BEND.KIND" target="_blank"> KIND keyword</a> in these sections is CHARM and not HARMONIC as I wrongly assumed. So you have to take care which KIND of forcefield you are using when you set these parameters.</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best regards</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> </div> <div> <div> <div> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt;margin-left:72.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><span class="MsoHyperlink">cp...@googlegroups.com</span> <<span class="MsoHyperlink">cp...@googlegroups.com</span>> on behalf of Léon Luntadila Lufungula <<span class="MsoHyperlink">Leon.luntad...@uantwerpen.be</span>><br> <b>Date: </b>Friday, 12 January 2024 at 12:24<br> <b>To: </b>cp2k <<span class="MsoHyperlink">cp...@googlegroups.com</span>><br> <b>Subject: </b>Re: [CP2K:19734] Correct TIP3P parameters</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt">Hi Matthias,<o:p></o:p></span></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt">Thanks for clarifying this for me. It was indeed a bit confusing, but I'm happy that I have a clear answer now!<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt">Kind regards,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt;margin-left:72.0pt"> <span style="font-size:11.0pt">Léon<o:p></o:p></span></p> </div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt">On Friday 12 January 2024 at 11:08:26 UTC+1 Krack Matthias wrote:<o:p></o:p></span></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">Hi Léon</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">Yes, 110 kcalmol*rad^-2 and 900 kcal*Angstrom^-2 are correct. Note, that the inputs in cp2k/tests are for code regression testing and the parameters used therein are not reliable by contrast to the example inputs given in the exercises. Unfortunately, many regression tests use this incorrect flexible TIP3P force field. This is most likely a copy-paste error which is indeed confusing for users. I will fix that.</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">Best </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> </div> <div> <div> <div> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt;margin-left:108.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><span class="MsoHyperlink">cp...@googlegroups.com</span> <<span class="MsoHyperlink">cp...@googlegroups.com</span>> on behalf of Léon Luntadila Lufungula <<span class="MsoHyperlink">Leon.luntad...@uantwerpen.be</span>><br> <b>Date: </b>Friday, 12 January 2024 at 10:09<br> <b>To: </b>cp2k <<span class="MsoHyperlink">cp...@googlegroups.com</span>><br> <b>Subject: </b>Re: [CP2K:19729] Correct TIP3P parameters</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span style="font-size:11.0pt">Hi Alin and Matthias,<o:p></o:p></span></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span style="font-size:11.0pt">Thanks for the quick reply, I didn't know that! If so, the 110/900 combination in the water.inp file should be correct then right? Still, in a lot of input files in the tests folder like for example cp2k/tests/Fist/regtest-4/H2O-1.inp (see attachment) the combination 55/450 is used. Can you explain why this is the case then?<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span style="font-size:11.0pt">Kind regards,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span style="font-size:11.0pt">Léon<o:p></o:p></span></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span style="font-size:11.0pt">On Friday 12 January 2024 at 10:02:01 UTC+1 Krack Matthias wrote:<o:p></o:p></span></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt">Dear Léon</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt">Note that LAMMPS uses a d</span><span style="font-size:11.0pt"><a href="https://docs.lammps.org/angle_harmonic.html" target="_blank"><span lang="EN-US">ifferent potential definition</span></a></span><span lang="EN-US" style="font-size:11.0pt">. By contrast to CP2K, LAMMPS includes the prefactor ½ into the constant K.</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt">HTH</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> </div> <div> <div> <div> <div> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt;margin-left:144.0pt"> <b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From: </span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><span class="MsoHyperlink">cp...@googlegroups.com</span> <<span class="MsoHyperlink">cp...@googlegroups.com</span>> on behalf of Léon Luntadila Lufungula <<span class="MsoHyperlink">Leon.luntad...@uantwerpen.be</span>><br> <b>Date: </b>Friday, 12 January 2024 at 09:53<br> <b>To: </b>cp2k <<span class="MsoHyperlink">cp...@googlegroups.com</span>><br> <b>Subject: </b>[CP2K:19726] Correct TIP3P parameters</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt">Dear all,<o:p></o:p></span></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt">Just a quick question about the parameters for the TIP3P forcefield. In the example files (see attached water.inp) of the <a href="https://www.cp2k.org/exercises:2019_uzh_acpc2:ex02" target="_blank">exercise</a> on molecular simulation of water the TIP3P model is used to simulate water. In the input file, I noticed that the force constant of the H-O-H bend and the H-O bond are 110 rad^-2kcalmol and 900 angstrom^-2kcalmol, respectively. However, when looking online for the parameters like on the <a href="https://docs.lammps.org/Howto_tip3p.html" target="_blank">lammps documentation</a>, I find that these values are actually half of what is defined in the input, i.e., 55 rad^-2kcalmol and 450 angstrom^-2kcalmol, respectively... Is this indeed an error in the input file or am I missing something here? Most water input files I see in the tests/Fist folder also contain the smaller values for the force constants.<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt"> <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt">Kind regards,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt">Léon<o:p></o:p></span></p> </div> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt">-- <o:p></o:p></span></p> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt">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 <o:p></o:p></span></p> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt"><span class="MsoHyperlink">cp2k+uns...@googlegroups.com</span>.<o:p></o:p></span></p> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt"><br> To view this discussion on the web visit <o:p></o:p></span></p> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:144.0pt"> <span style="font-size:11.0pt"><a href="https://groups.google.com/d/msgid/cp2k/2bed3d68-2c9d-4ceb-8672-208cfe7d0fd8n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/2bed3d68-2c9d-4ceb-8672-208cfe7d0fd8n%40googlegroups.com</a>.<o:p></o:p></span></p> </div> </div> </div> </div> </blockquote> </div> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span style="font-size:11.0pt">-- <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 <span class="MsoHyperlink">cp2k+uns...@googlegroups.com</span><o:p></o:p></span></p> </div> </div> </div> </div> <div> <div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:108.0pt"> <span style="font-size:11.0pt">.<br> To 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