Hi all,<br />
I generated a 3D free energy surface plot of my system. I observed an unexpected result: the simulation sampled an additional state that appears to be lower in energy than the reactant. This is surprising, as the reactant is expected to be the lower-energy species.
<br />
Upon further inspection, this new state resembles the product of the reaction. However, based on the previous study—specifically the glucose ring-opening mechanism described in DOI: 10.1021/jp402739q—the product should be higher in energy than the reactant.
<br /><br />
I would appreciate any insights into why this lower-energy product-like state might be appearing in the simulation, or if this could indicate an alternative reaction pathway or artifact in the sampling.<br /><br />Thank you.<br />Mawuli<br /><br /><br /><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, May 21, 2025 at 12:16:00 PM UTC-4 mawuli deegbey 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 dir="auto">Great and thank you for the explanation. </div><div dir="auto"><br></div><div dir="auto">Mawuli </div><div><br><div class="gmail_quote"></div></div><div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, May 21, 2025 at 11:29 AM Marcella Iannuzzi <<a href data-email-masked rel="nofollow">marci...@gmail.com</a>> wrote:<br></div></div></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;padding-left:1ex;border-left-color:rgb(204,204,204)">Hi Mawuli<div><br></div><div>It is exactly thanks to the accumulation of additional sampling that the shape of the FES changes. </div><div>This is the scope of metadynamics. I do not see anything strange in the plots, actually it seems to work pretty well.</div><div><br></div><div>Regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, May 21, 2025 at 5:17:44 PM UTC+2 Mawuli wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)">Hi Marcella,<br><div><br></div><div>
My goal is to analyze the convergence of my simulations.
<br>I’m trying to figure out why the free energy surface in dataset 11 shows a higher energy well compared to datasets 9 and 10, despite being a continuation, and if such cases do occur.</div><div><br></div><div>
Yes, I restarted the metadynamics simulations to collect additional data.
<br></div><div><br>Thank you.</div><div>Mawuli</div><br><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, May 21, 2025 at 4:26:06 AM UTC-4 Marcella Iannuzzi wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)">Hi ...<div>I am not sure of understanding your question correctly. </div><div>If you are restarting metadynamics and collecting more data, the earlier sampling was simply not converged yet. </div><div>Regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, May 21, 2025 at 9:05:51 AM UTC+2 Mawuli wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)"><div>Hi,</div><div><br>Could someone please help me figure out why my well-tempered metadynamics sampled a higher energy well after sampling a lower one? <br>For instance, within the range of 0.5 to 1.0, Data 11 (purple color) shows a higher energy than Data 8 to Data 10. After another sampling, a lower energy is obtained for Data 12. <br></div><div><br>I generated all these data points (fes.dat) using the CP2K graph tool. <br><br></div><div>Thank you.</div><div><br></div><br></blockquote></div></blockquote></div></blockquote></div>
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