<div>Dear Marcella and <span>Ivan , <br /></span></div><div><span>I have been trying to do the above simulation for sometimes now. Setting values hasn't been easy for the parameters. As per my understanding, I have tried a few possible values for the parameters. <br /></span></div><div><span>Sample input is given below. <br /></span></div><div> &COLVAR<br /> &COORDINATION<br /> ATOMS_FROM 2 <br /> ATOMS_TO 35 <br /> R0 2.6 <br /> NN 6 <br /> ND 12 <br /> &END COORDINATION<br /> &END COLVAR<br /> &COLVAR<br /> &HYDRONIUM_DISTANCE<br /> OXYGENS 1..32 <br /> HYDROGENS 33..96 <br /> LAMBDA 20.0 <br /> NH 2.2<br /> NN 0.56<br /> PF 6 <br /> PM 8 <br /> POH 6 <br /> QF 12 <br /> QM 16 <br /> QOH 12 <br /> ROH 2.6 <br /> &END HYDRONIUM_DISTANCE<br /> &END COLVAR</div><div>I am only focusing on a O-H bond instead of the water molecule. So in coordination, I have defined a single H against O. Is that a problem ? <br /></div><div>Also, I am not sure if I have understood meanings of NH, PM and QM . I do not understand what is meant by M function. While in the original work, the M function is implemented in equation 3. Do we also need M function hydronium distance as well ? <br /></div><div>Any suggestions will be helpful. <br /></div><div>Sincerely <br /></div><div>Bijaya <br /></div><br /><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, July 24, 2025 at 11:45:17 AM 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;"><div style="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><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-feature-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-feature-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-feature-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-feature-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-feature-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-feature-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-feature-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-feature-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"></blockquote></div></div></div><div style="line-break:after-white-space"><div><div><blockquote type="cite"><div>On Jul 24, 2025, at 07:41, bijaya pathak <<a href data-email-masked rel="nofollow">bijayap...@gmail.com</a>> wrote:</div><br></blockquote></div></div></div><div style="line-break:after-white-space"><div><div><blockquote type="cite"><div><div style="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;text-decoration:none">Dear Ivan, </div><div style="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;text-decoration:none">Thank you so much for your reply. It does help.</div><div style="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;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> </span><br></div><div style="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;text-decoration:none">Thanks and regards</div><div style="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;text-decoration:none">Bijaya</div><br style="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;text-decoration:none"><div class="gmail_quote" style="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;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" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://www.nature.com/articles/s41467-024-53186-5&source=gmail&ust=1756821018577000&usg=AOvVaw0zSioYWUj3wBj-Za0xZtyL">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> </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> </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> </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=1756821018577000&usg=AOvVaw0R64LJkjKzit2vO5J3doTR">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=1756821018577000&usg=AOvVaw1nIA-EGLJXqdjD2lCnCYTK"></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=1756821018577000&usg=AOvVaw1fZznszCwsIww37r8u13bF"><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=1756821018577000&usg=AOvVaw16gc2MZgSpCPwM26oT9DVK"><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=1756821018577000&usg=AOvVaw2K7cwHJnS-n3cwYl-DG-tn"><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=1756821018577000&usg=AOvVaw1SnHqXwZ8OoQk5z9Lm1vKn"><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=1756821018577000&usg=AOvVaw1iTKwJzCMR_BhLnjlxHVkx"><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=1756821018577000&usg=AOvVaw3BtG8f5dG8T0TJQl6MPhsk"><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=1756821018577000&usg=AOvVaw0qaYENVsCgPhf-Ph_0kMFM"><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=1756821018577000&usg=AOvVaw0AwX7zT7lTm5UmNWwBbTbu"><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=1756821018577000&usg=AOvVaw0VlTCe5rh9P1Mrf69piMi9"><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=1756821018577000&usg=AOvVaw0DQ6d1T-uxzZOp_isdSN1g"><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=1756821018577000&usg=AOvVaw34OcrH-nnPx4A8GzymDxmo"><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=1756821018577000&usg=AOvVaw2EyDETwe7uIlvSo8Pk9zHL"><span>ROH</span></a></p></li></ul></span>Greatly appreciate any suggestions</div><div>Thanks<span> </span><br></div><div>Bijaya</div></blockquote></div></blockquote></div><div style="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;text-decoration:none"><br></div></div></blockquote></div></div></div><div style="line-break:after-white-space"><div><div><blockquote type="cite"><div><span style="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;text-decoration:none;float:none;display:inline!important">--<span> </span></span><br style="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;text-decoration:none"><span 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