Dear B<span style="caret-color: rgb(32, 33, 36); color: rgb(32, 33, 36); font-family: Roboto, Arial, sans-serif; letter-spacing: 0.25px;">ijaya</span><br /><br /><div>The hydronium distance defined in (J. Am. Chem. Soc.,128, 2006, 11318) is not trivial to be implemented in CP2K alone.</div><div>You can give a look to the supporting information of </div><div><br /></div><div>https://www.nature.com/articles/s41467-024-53186-5<br /></div><div><br /></div><div>There, PLUMED plug-in was used to code the CV to be then used in combination with CP2K. </div><div>You may take inspiration.</div><div>If I recall well, in the supporting information there is also an input example. </div><div><br /></div><div>Hope it helps.</div><div>Best</div><div>Ivan</div><div><br /></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday, July 21, 2025 at 3:00:16 PM UTC+3 bijaya pathak 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>Dear all, <br></div><div>I would like to know the function that's been used to describe the CV Hydronium_distance which appears to consider the distance between the distance between hydroxide ion and hydronium ion. There are lots of parameters given in the subsection I believe is derived from (J. Am. Chem. Soc.,128, 2006, 11318).</div><div>Can anyone help me understand what do these parameters mean ? <br></div><div><br></div><div><p>Section to define the formation of a hydronium as a collective variable. Distance between hydronium and hydroxide ion Experimental at this point, i.e. not proved to be an effective collective variable. <span>[<a href="https://github.com/cp2k/cp2k/blob/master/src/input_cp2k_colvar.F#L1402" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://github.com/cp2k/cp2k/blob/master/src/input_cp2k_colvar.F%23L1402&source=gmail&ust=1753356403182000&usg=AOvVaw0kS57Fs5xGVIo5fckW9YVf">Edit on GitHub</a>]</span></p> <span> <span>Keywords<a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#keywords" title="Link to this heading" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23keywords&source=gmail&ust=1753356403182000&usg=AOvVaw2ZJyTaOHJyGfY43lspkq4C"></a></span> <ul><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.HYDROGENS" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.HYDROGENS" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.HYDROGENS&source=gmail&ust=1753356403182000&usg=AOvVaw1B0xPeBu-1TftA2WNfaM8Z"><span>HYDROGENS</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.LAMBDA" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.LAMBDA" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.LAMBDA&source=gmail&ust=1753356403182000&usg=AOvVaw2Iaea5C_5Wzq6u1xGnMi1b"><span>LAMBDA</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.NH" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.NH" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.NH&source=gmail&ust=1753356403182000&usg=AOvVaw1Tg8oNXRNrT66Fcn8_qJFg"><span>NH</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.NN" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.NN" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.NN&source=gmail&ust=1753356403182000&usg=AOvVaw3dB6ajHR_2GsOaZ2Io9_Lp"><span>NN</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.OXYGENS" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.OXYGENS" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.OXYGENS&source=gmail&ust=1753356403182000&usg=AOvVaw0qz-BIIbvsNXdiLuzj5AIS"><span>OXYGENS</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.PF" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.PF" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.PF&source=gmail&ust=1753356403182000&usg=AOvVaw0nT-Z5Evt1VgBMNpnDLHVJ"><span>PF</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.PM" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.PM" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.PM&source=gmail&ust=1753356403182000&usg=AOvVaw1JsUcnyHPNH2R0FnHRFfYa"><span>PM</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.POH" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.POH" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.POH&source=gmail&ust=1753356403182000&usg=AOvVaw1UqfGjS32nUUAlLoWfRCBc"><span>POH</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QF" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QF" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QF&source=gmail&ust=1753356403182000&usg=AOvVaw1vjZ2noWAj0Ws94s2H_ngH"><span>QF</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QM" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QM" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QM&source=gmail&ust=1753356403182000&usg=AOvVaw2kZtIKtG411xiSW2ZUfXzs"><span>QM</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QOH" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QOH" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QOH&source=gmail&ust=1753356403182000&usg=AOvVaw0QBjorNZIUI31Ri5YoflDE"><span>QOH</span></a></p></li><li><p><a href="https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.ROH" title="CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.ROH" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html%23CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.ROH&source=gmail&ust=1753356403182000&usg=AOvVaw2HnzwasVm0S7s6gpm5MY1h"><span>ROH</span></a></p></li></ul> </span>Greatly appreciate any suggestions</div><div>Thanks <br></div><div>Bijaya</div></blockquote></div> <p></p> -- <br 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