<div>Dear Ivan, </div><div>Thank you so much for your reply. It does help.</div><div>To clarify what you said, If I use the plumed plug-in with cp2k, it should work if I define my functions in plumed.dat and supply it to cp2k ? <br /></div><div>Thanks and regards</div><div>Bijaya</div><br /><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, July 23, 2025 at 5:05:01 PM UTC+5:30 Ivan Gladich 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;">Dear B<span style="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><a href="https://www.nature.com/articles/s41467-024-53186-5" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://www.nature.com/articles/s41467-024-53186-5&source=gmail&ust=1753418339883000&usg=AOvVaw05tB7BmRUJseZfR2u_a9NM">https://www.nature.com/articles/s41467-024-53186-5</a><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw0gCU1jlPE3fjRs6Z5BrQ24">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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw3J7NmUzZEACLuaGL_0uDVk"></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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw046FEvujsyzIPULzOBTf1h"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw09rC6oGbDoAC8A0-TJX_ty"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw1vOQ6F3J89B03zlveXazDx"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw3nXXcgDReBMBf3kMUemVgD"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw3Vg9qbQmDTPcx_IB7oe-cL"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw3hBskG1BtTr_tJ5jG9TKc6"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw1KESZisec6JOJeV2chVHi7"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw1agR9eRPEWkbcupRXqFGdE"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw0ibxrI8ggHZN69tq6Satsz"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw05h61iIxTuRUVodbMYMHlN"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw3eftkl2MQw8x8US107uDWa"><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" rel="nofollow" target="_blank" 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=1753418339883000&usg=AOvVaw25wFkWlLC8xygd9SU95lJL"><span>ROH</span></a></p></li></ul> </span>Greatly appreciate any suggestions</div><div>Thanks <br></div><div>Bijaya</div></blockquote></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 visit <a href="https://groups.google.com/d/msgid/cp2k/528e3146-65f0-4990-9279-eb42a2045c69n%40googlegroups.com?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/528e3146-65f0-4990-9279-eb42a2045c69n%40googlegroups.com</a>.<br />