<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi,<div><br></div><div>You have two options</div><div>1) Use CP2k implementation as Marcella previously posted to you. (I did not know was implemented directly in CP2K. Thanks)</div><div>2) Use PLUMED plug-in. Your CP2K should be compiled with the option <span style="font-size: 12pt; font-family: "Times New Roman", serif; color: rgb(0, 176, 80);"> --with-plumed=install </span><span style="font-family: -webkit-standard; font-size: medium;"></span><br id="lineBreakAtBeginningOfMessage"><div>If this is the case, you can provide the plumed.dat with all the functions. (Testing and tuning is necessary also in this case)</div><div>In the MOTION section as follow</div><div><br></div><div><p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-variant-emoji: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;"><span style="font-variant-ligatures: no-common-ligatures"> &FREE_ENERGY</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-variant-emoji: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;"><span style="font-variant-ligatures: no-common-ligatures"> &METADYN</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-variant-emoji: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;"><span style="font-variant-ligatures: no-common-ligatures"> USE_PLUMED .TRUE.</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-variant-emoji: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;"><span style="font-variant-ligatures: no-common-ligatures"> PLUMED_INPUT_FILE plumed.dat</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-variant-emoji: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;"><span style="font-variant-ligatures: no-common-ligatures"> &END METADYN</span></p>
<p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-variant-emoji: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;"><span style="font-variant-ligatures: no-common-ligatures"> &END FREE_ENERGY</span></p><p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-variant-emoji: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;"><span style="font-variant-ligatures: no-common-ligatures"><br></span></p><p style="margin: 0px; font-style: normal; font-variant-caps: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; font-size-adjust: none; font-kerning: auto; font-variant-alternates: normal; font-variant-ligatures: normal; font-variant-numeric: normal; font-variant-east-asian: normal; font-variant-position: normal; font-variant-emoji: normal; font-feature-settings: normal; font-optical-sizing: auto; font-variation-settings: normal;"><br></p></div><div>Which solution is easier? </div><div>Not sure, depends on your problem and system.</div><div><br></div><div>Hope it helps</div><div>Best</div><div>Ivan</div><div><br></div><div><br></div><div><br><blockquote type="cite"><div>On Jul 24, 2025, at 07:41, bijaya pathak <bijayapathak85@gmail.com> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">Dear Ivan, </div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">Thank you so much for your reply. It does help.</div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">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 ?<span class="Apple-converted-space"> </span><br></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">Thanks and regards</div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">Bijaya</div><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div class="gmail_quote" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><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: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: 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: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div>Dear all,<span class="Apple-converted-space"> </span><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 ?<span class="Apple-converted-space"> </span><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 class="Apple-converted-space"> </span><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<span class="Apple-converted-space"> </span><br></div><div>Bijaya</div></blockquote></div></blockquote></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br class="webkit-block-placeholder"></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">--<span class="Apple-converted-space"> </span></span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 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