<div>Dear Nam<b><br></b></div><div><br></div>I run the command<b> "graph.popt -ndim 3 -ndw 1 2 3 -file metad.restart -find-path -point-a CVs(point A) -point-b CVs(point B) -cp2k", But get errors :</b><div><div style=""><b><br></b></div><div style=""><b>forrtl: severe (59): list-directed I/O syntax error, unit -5, file Internal List-Directed Read</b></div><div style=""><b>Image PC Routine Line Source </b></div><div style=""><b>graph.popt 00000000004584DE for__io_return Unknown Unknown</b></div><div style=""><b>graph.popt 000000000047B6ED for_read_int_lis_ Unknown Unknown</b></div><div style=""><b>graph.popt 0000000000479E56 for_read_int_lis Unknown Unknown</b></div><div style=""><b>graph.popt 000000000040B740 Unknown Unknown Unknown</b></div><div style=""><b>graph.popt 00000000004B4CD2 Unknown Unknown Unknown</b></div><div style=""><b>libc-2.17.so 00002B5BED02C555 __libc_start_main Unknown Unknown</b></div><div style=""><b>graph.popt 0000000000409729 Unknown Unknown Unknown</b></div><br></div><div>Do you know why? </div><div>Thanks advance</div><div><br></div><div>Best</div><div>Vaclav</div><div class="gmail_quote"><div dir="auto" class="gmail_attr">在2021年2月18日星期四 UTC+8 上午11:02:20<trann...@gmail.com> 写道：<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Dear Prof. Marcella<div><br></div><div>Thank you for your quick reply. Your reference is very helpful.</div><div><br></div><div>I just realized that, the <b>graph.popt</b> module could be used to scan the minima in the whole FES.</div><div><b>graph.popt -ndim 3 -ndw 1 2 3 -file metad.restart -find-minima -cp2k</b><br></div><div>Then the MEP connecting two selected minima can be calculated using the same module. </div><div><b>graph.popt -ndim 3 -ndw 1 2 3 -file metad.restart -find-path -point-a CVs(point A) -point-b CVs(point B) -cp2k</b></div><div><i><br></i>Best regards</div><div>Nam</div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, 16 February 2021 at 7:46:29 pm UTC+11 Marcella Iannuzzi 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">Dear Nam,<div><br></div><div>The FES can be integrated in some directions in order to reduce the dimensionality and to be able to plot a profile or a contour along one or two coordinates only. </div><div>Obviously information along the integrated out coordinates will be lost. </div><div>As alternative, one can find minimum energy pathways connecting given points scanning the whole FES</div><div>The resulting pathway is a function of all CVs.</div><div><br></div><div>The method works in principle with any number of CVs, </div><div>but increasing the number of CVs makes the time required for exploring the FES longer and the interpretation of the results more difficult. </div><div><br></div><div>You can find in the literature discussions on how to analyse the CVs space.</div><div>An example in <a href="https://doi.org/10.1063/1.5027528" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=zh-CN&q=https://doi.org/10.1063/1.5027528&source=gmail&ust=1636087524330000&usg=AFQjCNGSnnStP3gkjnev1693Sa3pCjAiKg">https://doi.org/10.1063/1.5027528</a></div><div><br></div><div>Regards</div><div>Marcella <br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday, February 15, 2021 at 3:32:38 PM UTC+1 <a rel="nofollow">trann...@gmail.com</a> 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">Hi,<div><br></div><div>I have done a metadynamics calculation with cp2k using two collective variables (CVs). It is very intuitive in this case to plot the contour of the free energy corresponding to the two collective variable. From the contour plot I can easily define the minima and the MEP between them. I can also calculate the barrier energy from the MEP.<br></div><div><br></div><div>Now I want to do a simulation with three collective variable. Is there any easy way to find the minima as well as MEP between those minima?. I found it has been done in the ref: <a href="https://pubs.acs.org/doi/10.1021/acscatal.9b00239" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=zh-CN&q=https://pubs.acs.org/doi/10.1021/acscatal.9b00239&source=gmail&ust=1636087524330000&usg=AFQjCNFLPewjZfLrfD5dOcY-N87URDPoyQ">https://pubs.acs.org/doi/10.1021/acscatal.9b00239</a>, but I don't know how.</div><div>Also, If I want to increase the number of CVs i.e., into 4 or 5. Does the method still work?</div><div><br></div><div>Best regards</div><div>Nam</div></blockquote></div></blockquote></div></blockquote></div>
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