<div dir="ltr">I am attempting to study the FES for a SN2 reaction (i.e. a negative ion (F-) leaves the molecule and becomes solvated, while an OH- takes its place). In attempting to reproduce the results of an article using CP2K's metadynamics, I am seeing the F being driven away from the molecule, but not seeing it being solvated. I presently have the COLVARS declared as below. <div><br></div><div>I have two concerns:</div><div>1.) Is the coordination COLVAR driving the O in water away from the F ion?</div><div>2.) Is there a way to have the COLVAR show up in the free energy surfaces generated by the fes.sopt code but not be used with hills? Simply leaving the coordination COLVAR out of the motion section, but still declared in the &SUBSYS section eliminated it from the FES generated by the fes.sopt program altogether.<br></div><div><div class="prettyprint" style="background-color: rgb(250, 250, 250); border: 1px solid rgb(187, 187, 187); word-wrap: break-word;"><code class="prettyprint"><div class="subprettyprint"><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">MOTION<br>  </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">FREE_ENERGY<br><br><br>   METHOD METADYN <br><br><br>   </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">METADYN <br><br>    DO_HILLS </span><span style="color: #660;" class="styled-by-prettify">.</span><span style="color: #000;" class="styled-by-prettify">TRUE</span><span style="color: #660;" class="styled-by-prettify">.</span><span style="color: #000;" class="styled-by-prettify"> <br><br>    WW </span><span style="color: #660;" class="styled-by-prettify">[</span><span style="color: #000;" class="styled-by-prettify">hartree</span><span style="color: #660;" class="styled-by-prettify">]</span><span style="color: #000;" class="styled-by-prettify"> </span><span style="color: #066;" class="styled-by-prettify">1.0E-2</span><span style="color: #000;" class="styled-by-prettify"> <br><br>    NT_HILLS </span><span style="color: #066;" class="styled-by-prettify">15</span><span style="color: #000;" class="styled-by-prettify"> <br><br><br>   </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">METAVAR <br><br>     COLVAR </span><span style="color: #066;" class="styled-by-prettify">1</span><span style="color: #000;" class="styled-by-prettify"> <br><br>     SCALE </span><span style="color: #066;" class="styled-by-prettify">0.08</span><span style="color: #000;" class="styled-by-prettify"> <br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> METAVAR <br><br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">METAVAR <br><br>     COLVAR </span><span style="color: #066;" class="styled-by-prettify">2</span><span style="color: #000;" class="styled-by-prettify"> <br><br>     SCALE </span><span style="color: #066;" class="styled-by-prettify">0.08</span><span style="color: #000;" class="styled-by-prettify"> <br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> METAVAR <br><br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">METAVAR <br><br>     COLVAR </span><span style="color: #066;" class="styled-by-prettify">3</span><span style="color: #000;" class="styled-by-prettify"> <br><br>     SCALE </span><span style="color: #066;" class="styled-by-prettify">0.08</span><span style="color: #000;" class="styled-by-prettify"> <br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> METAVAR<br>  </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> FREE_ENERGY<br></span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> MOTION</span></div></code></div><div>and in the &FORCE_EVAL section as:</div><div class="prettyprint" style="background-color: rgb(250, 250, 250); border: 1px solid rgb(187, 187, 187); word-wrap: break-word;"><code class="prettyprint"><div class="subprettyprint"><span style="color: #000;" class="styled-by-prettify">  </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">SUBSYS<br><br>     </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">CELL <br><br>      ABC </span><span style="color: #066;" class="styled-by-prettify">12.97658</span><span style="color: #000;" class="styled-by-prettify"> </span><span style="color: #066;" class="styled-by-prettify">12.90794</span><span style="color: #000;" class="styled-by-prettify"> </span><span style="color: #066;" class="styled-by-prettify">12.97688</span><span style="color: #000;" class="styled-by-prettify"> <br><br>      PERIODIC XYZ <br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> CELL <br> <br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">COLVAR <br><br>     </span><span style="color: #660;" class="styled-by-prettify">!</span><span style="color: #000;" class="styled-by-prettify">P to F<br> <br>     </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">DISTANCE <br><br>      ATOMS </span><span style="color: #066;" class="styled-by-prettify">12</span><span style="color: #000;" class="styled-by-prettify"> </span><span style="color: #066;" class="styled-by-prettify">18</span><span style="color: #000;" class="styled-by-prettify"> <br><br>     </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> DISTANCE <br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> COLVAR <br><br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">COLVAR <br><br>     </span><span style="color: #660;" class="styled-by-prettify">!</span><span style="color: #000;" class="styled-by-prettify">P to O <br><br>     </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">DISTANCE <br><br>      ATOMS </span><span style="color: #066;" class="styled-by-prettify">12</span><span style="color: #000;" class="styled-by-prettify"> </span><span style="color: #066;" class="styled-by-prettify">13</span><span style="color: #000;" class="styled-by-prettify"> <br><br>     </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> DISTANCE <br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> COLVAR <br> <br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">COLVAR <br><br>     </span><span style="color: #660;" class="styled-by-prettify">!</span><span style="color: #000;" class="styled-by-prettify">see </span><span style="color: #066;" class="styled-by-prettify">10.1021</span><span style="color: #660;" class="styled-by-prettify">/</span><span style="color: #000;" class="styled-by-prettify">jp301490k </span><span style="color: #008;" class="styled-by-prettify">for</span><span style="color: #000;" class="styled-by-prettify"> ND NN R0 parameter meaning <br><br>     </span><span style="color: #660;" class="styled-by-prettify">!</span><span style="color: #000;" class="styled-by-prettify"> P to O </span><span style="color: #008;" class="styled-by-prettify">in</span><span style="color: #000;" class="styled-by-prettify"> water <br><br>     </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">COORDINATION <br><br>      ND </span><span style="color: #066;" class="styled-by-prettify">12</span><span style="color: #000;" class="styled-by-prettify"> <br><br>      NN </span><span style="color: #066;" class="styled-by-prettify">6</span><span style="color: #000;" class="styled-by-prettify"> <br><br>      R0 </span><span style="color: #660;" class="styled-by-prettify">[</span><span style="color: #000;" class="styled-by-prettify">bohr</span><span style="color: #660;" class="styled-by-prettify">]</span><span style="color: #000;" class="styled-by-prettify"> </span><span style="color: #066;" class="styled-by-prettify">3.0</span><span style="color: #000;" class="styled-by-prettify"> <br><br>      KINDS_FROM P <br><br>      KINDS_TO </span><span style="color: #606;" class="styled-by-prettify">Ow</span><span style="color: #000;" class="styled-by-prettify"> <br><br>     </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> COORDINATION <br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> COLVAR<br><br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #000;" class="styled-by-prettify">COORD<br>      </span><span style="color: #660;" class="styled-by-prettify">...</span><span style="color: #000;" class="styled-by-prettify">    <br>    </span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> COORD<br><br></span><span style="color: #660;" class="styled-by-prettify">&</span><span style="color: #008;" class="styled-by-prettify">END</span><span style="color: #000;" class="styled-by-prettify"> SUBSYS</span></div></code></div><div><br><br></div></div></div>