<div dir="ltr">Thanks for the reply.<div> </div><div>I believe that I should clarify the matter at hand. The Coordination COLVAR starts very near zero, but it should since the F is still attached to the rest of the molecule. It is only after the F detaches that the waters will actually be able to solvate the F ion. My concern is that the potential well that the solvated F ion resides in is being filled by the gaussians and preventing the solvation from occurring after F has moved away from the molecule. The study I am trying to replicate used the coordination as a collective variable (Unfortunately, the authors won't respond to my queries). The study offers a lot of details and not mention they did anything out of the ordinary. I am curious why even after 10ps I don't see the solvation occurring despite it being driven to occur. But my concern is that it might be driven away from the solvated state. On Monday, May 11, 2015 at 2:43:14 PM UTC-6, Marcella Iannuzzi wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr"> Hi Cristopher,<div> </div><div> It is possible that the MTD potential is pushing your system too fast away from equilibrium, without allowing the correct reorganisation of the solvent. This happens when the hills are too large and new hills are added too frequently. </div><div>Difficult to be more specific and guess which COLVAR is responsible without having the output, but if the coordination with Ow does not change, it is not the coordination that is driving the system. </div><div>The FES is reconstructed using the hills building up the MTD potential. These latter are defined in terms of the COLVARs used for the MTD.</div><div>You can define more COLVARs and use only some of them as METAVARs, though. The additional COLVARs obviously play no role in MTD and their values are not recorded in the MTD output files. </div><div>Anyway structural parameters can be monitored from the post processing of the trajectory. </div><div> </div><div>Kind regards</div><div>Marcella</div><div> On Monday, May 11, 2015 at 9:05:24 PM UTC+2, Christopher O'Brien wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><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> </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. </div><div><div style="background-color:rgb(250,250,250);border:1px solid rgb(187,187,187);word-wrap:break-word"><code><div>&MOTION &FREE_ENERGY METHOD METADYN &METADYN DO_HILLS .TRUE. WW [hartree] 1.0E-2 NT_HILLS 15 &METAVAR COLVAR 1 SCALE 0.08 &END METAVAR &METAVAR COLVAR 2 SCALE 0.08 &END METAVAR &METAVAR COLVAR 3 SCALE 0.08 &END METAVAR &END FREE_ENERGY &END MOTION</div></code></div><div>and in the &FORCE_EVAL section as:</div><div style="background-color:rgb(250,250,250);border:1px solid rgb(187,187,187);word-wrap:break-word"><code><div> &SUBSYS &CELL ABC 12.97658 12.90794 12.97688 PERIODIC XYZ &END CELL &COLVAR !P to F &DISTANCE ATOMS 12 18 &END DISTANCE &END COLVAR &COLVAR !P to O &DISTANCE ATOMS 12 13 &END DISTANCE &END COLVAR &COLVAR !see 10.1021/jp301490k for ND NN R0 parameter meaning ! P to O in water &COORDINATION ND 12 NN 6 R0 [bohr] 3.0 KINDS_FROM P KINDS_TO Ow &END COORDINATION &END COLVAR &COORD ... &END COORD &END SUBSYS</div></code></div><div> </div></div></div></blockquote></div></div></blockquote></div></div>