<div dir="ltr"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Hi,</div><div><br></div><div> I have set up and run a metadynamics simulation using two bond distances as the CV where the two bonds are forming during the reaction. The calculation finished with my desired prediction. Now I am trying to analyze the data and draw the free energy surface from the minimum energy path. I am using the graph.psmp tool of CP2K for doing this. I have generated the fes.dat file and mep.dat file. But I am facing some problems to plot the FES. Could anyone help me to do the following things?</div><div><br></div><div>I want to draw the FES between energy and bond distance. </div><div>How can I extract the transition state structure from the free energy surface? Calculate the free energy barrier etc.</div><div>How to get the bond distance which I have used as CV, from the COLVAR.metadynLog file.</div><div><br></div><div>Please someone assist me regarding this problem.</div><div><br></div><div>best regards,</div><div>Tamal</div><div dir="ltr"><div><br></div></div></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Feb 2, 2024 at 3:55 AM Marcella Iannuzzi <<a href="mailto:marci.akira@gmail.com">marci.akira@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>Hi ..</div><div><br></div>In the COLVAR description you can define POINT as POINT / TYPE GEO_CENTER of a list of POINT / ATOMS and use POINT / WEIGHTS if the atoms in the list have different masses and you want to use the COM<div>Then depending on the specific COLVAR (for example the DISTANCE), the definition uses the list of POINTS </div><div><br></div><div>Regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Friday, February 2, 2024 at 8:46:09 AM UTC+1 <a href="mailto:bijayap...@gmail.com" target="_blank">bijayap...@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>Dear all, <br></div><div>I'm trying to carryout a metadynamics simulation using COM-COM distance as my collective variable for a dimeric system. <br></div><div>I have done metadynamics simulations previously, but the CV was bond distance. <br></div><div>Can anyone please help me with defining COM-COM distance as CV for metadynamics ?</div><div>Thanking in advance. <br></div></blockquote></div>
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