<div dir="ltr">Dear Marcella, <div><br></div><div>Thank you for your help. It took me a lot of attempts but I managed to converge the calculation. </div><div><br></div><div>Thank you again!</div><div><br></div><div>Sara</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El jue, 22 sept 2022 a las 9:39, Marcella Iannuzzi (<<a href="mailto:marci.akira@gmail.com">marci.akira@gmail.com</a>>) escribió:<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><br></div><div><br></div>Dear Sara <div><br></div><div>Starting around step 50 the coordinates do not change anymore</div><div>Max. step size             =         0.0000000000</div><div>The gradient  above tolerance is only one. It is the x component of the force on atom 47, a hydrogen. </div><div>It remains practically constant for many steps.</div><div>It seems that the optimisation algorithm is not in the conditions of performing any CG step, and the SD gets stuck. </div><div>So since step 50 nothing changes in the structure.</div><div>I would try and change the optimiser to BFGS.</div><div><br></div><div>Kind regards</div><div>Marcella</div><div><br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, September 21, 2022 at 11:30:55 PM UTC+2 <a href="mailto:salla...@gmail.com" target="_blank">salla...@gmail.com</a> 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 dir="ltr">Dear Ivan, Victor and Marcella, <div><br></div><div>Thank you so much for your help. </div><div><br></div><div>I have been reading the bibliography you suggested and using your inputs and I almost optimised the heme group. I got to a point where the optimisation does not seem to converge but it is really close. </div><div><br></div><div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">--------<span>  </span>Informations at step = <span>  </span>114 ------------</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Optimization Method<span>        </span>= <span>                  </span>SD</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Total Energy <span>              </span>=<span>      </span>-517.5364879764</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Real energy change <span>        </span>= <span>        </span>0.0000000050</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Decrease in energy <span>        </span>= <span>                  </span>NO</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Used time<span>                  </span>=<span>              </span>460.425</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Convergence check :</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Max. step size <span>            </span>= <span>        </span>0.0000000000</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Conv. limit for step size<span>  </span>= <span>        </span>0.0010000000</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Convergence in step size <span>  </span>=<span>                  </span></span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">YES</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>RMS step size<span>              </span>= <span>        </span>0.0000000000</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Conv. limit for RMS step <span>  </span>= <span>        </span>0.0010000000</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Convergence in RMS step<span>    </span>=<span>                  </span></span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">YES</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Max. gradient<span>              </span>= <span>        </span>0.0012644252</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Conv. limit for gradients<span>  </span>= <span>        </span>0.0010000000</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Conv. for gradients<span>        </span>= <span>                  </span>NO</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>RMS gradient <span>              </span>= <span>        </span>0.0002927175</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Conv. limit for RMS grad.<span>  </span>= <span>        </span>0.0010000000</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span>  </span>Conv. in RMS gradients <span>    </span>=<span>                  </span></span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">YES</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span> </span>---------------------------------------------------</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">I have been playing a bit with the parameters but I haven't managed to make it work. </span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">Thanks again, </p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">Kind regards, </p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><br></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">Sara</p></div></div><br><div class="gmail_quote"></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El jue, 15 sept 2022 a las 17:57, Marcella Iannuzzi (<<a rel="nofollow">marci...@gmail.com</a>>) escribió:<br></div></div><div class="gmail_quote"><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 Sara<div><br></div><div>Before starting a geometry optimisation it is  good practice to get a converged single point calculation. </div><div>If I understand correctly from the output you posted, this was not the case. </div><div><br></div><div>I played a bit with the settings for your system and I got a converged single point calculation at the PBE level of theory </div><div>for the molecule charged --2 (see the attached file).</div><div><br></div><div>Kind regards</div><div>Marcella</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, September 13, 2022 at 4:00:25 PM UTC+2 <a rel="nofollow">salla...@gmail.com</a> 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 all, <div><br></div><div>I am having problems on a geometry optimisation of a heme group with Fe2+ using PBE in CP2K. My calculations run and the total energy is decreasing. However, the job has been running for almost a month and it doesn't seem to converge. </div><div><br></div><div>I am not an expert on CP2K nor on transition metals. I would really appreciate it if you could help me sort this out. I have  attached the restart file and the output for clarity. </div><div><br></div><div>Thanks a lot, </div><div><br></div><div><br></div><div>Sara</div></blockquote></div>

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