<div><br></div><div><br></div>Dear JHu<div><br></div><div>if you understand how the reconstruction of the FES works, you know that the Gaussian contributions to the metadynamics potential have a certain extension, hence they also contribute to parts of the CVs meatspace that do not correspond to points visited by the metatrajectory, which is the one reported in *-COLVAR.metadynLog. Moreover these Gaussian contributions sum up, and if the matadynamics settings are not properly chosen they might even produce misleading FES topographies. I cannot judge whether this is your case, but for sure it is to be expected that the minima on the FES are not exact points of the metatrajectory in *-COLVAR.metadynLog. If they are in completely unexpected regions, far from those most frequently visited by the trajectory, the metadynamics settings are most probably not properly chosen. </div><div><br></div><div>The -opt-path option of graph requires as input a path file, not the Hills file. </div><div><br></div><div>Regards</div><div>Marcella</div><div><br></div><div><br></div><div><br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, November 3, 2021 at 7:06:56 AM UTC+1 hujin...@gmail.com 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;"><br><div>Dear Marcella</div><div><br></div><div>Thanks and sorry to bother you again. I understand the fact that the FES generated by graph is reconstructed but the minima I got from graph which contain the CVs' values cannot be found in *-COLVAR.metadynLog. Is this situation normal?</div><div><br></div><div>And I tried another command line "graph.popt -ndim 2 -ndw 1 2Â Â
-opt-path
 *HILLS.metadynLog -orac". And it still went wrong as follows:<br></div><div><br></div><div> ABORT in metadyn_tools/graph.F:198 CPASSERT failed<br>forrtl: error (76): Abort trap signal</div><div><br>Image             PC               Routine           Line       Source            <br></div><div>graph.popt        0000000000500274 Unknown              Unknown Unknown<br>libpthread-2.17.s 00002B6FF116F630 Unknown              Unknown Unknown<br><a href="http://libc-2.17.so" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://libc-2.17.so&source=gmail&ust=1636012241462000&usg=AFQjCNGSYPBa4cZOQImIhL-L403k8znpKA">libc-2.17.so</a>      00002B6FF5641387 gsignal              Unknown Unknown<br><a href="http://libc-2.17.so" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://libc-2.17.so&source=gmail&ust=1636012241462000&usg=AFQjCNGSYPBa4cZOQImIhL-L403k8znpKA">libc-2.17.so</a>      00002B6FF5642A78 abort                Unknown Unknown<br>graph.popt        000000000044E345 base_hooks_mp_cp_         78 base_hooks.F<br>graph.popt        000000000040D97E MAIN__                   198 graph.F</div><div><br>graph.popt        000000000040CA62 Unknown              Unknown Unknown<br></div><div><a href="http://libc-2.17.so" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://libc-2.17.so&source=gmail&ust=1636012241462000&usg=AFQjCNGSYPBa4cZOQImIhL-L403k8znpKA">libc-2.17.so</a>      00002B6FF562D555 __libc_start_main    Unknown Unknown<br>graph.popt        000000000040C969 Unknown              Unknown Unknown<br>Aborted (core dumped)<br></div><div><br></div><div>Maybe you can give me some advice about the graph usage. Thanks in advance!</div><div><br></div><div>
<div>
<div>Regards</div><div>JHu</div></div></div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, November 2, 2021 at 10:05:10 PM UTC+8 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"><br>Dear JHu<div><br></div><div>Each minimum on the FES corresponds to specific values of the CVs, as you defined them. Hence, any structure for which the CVs take those values  belongs to the minimum. There is no one specific set of coordinates. </div><div><br></div><div>I expect that the points among which the path is calculated should be taken from the generated FES and not from the restart file. </div><div><br></div><div>Kind regards</div><div>Marcella</div><div><br></div><div><br></div><div> </div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, November 2, 2021 at 2:13:34 PM UTC+1 <a rel="nofollow">hujin...@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"><br>Dear Marcella<br><br><div>Really thanks for your reply. So, as for the first problem, do you know how to locate the exact minimum of FE and find the corresponding structure? Sorry that I have no idea about it.</div><div><br></div><div>As for the second, since the FES is reconstructed, the data of "-point-a" should belong to the *.restart file rather than the values I got from the first step
'graph.popt -ndim 2 -ndw 1 2 -file *.restart -find-minima -cp2k' , right?<br></div><div><br></div><div>
<div>Regards</div><div>JHu</div>
</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, November 2, 2021 at 4:35:49 PM UTC+8 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"><div><br></div>Dear JHu<div><br></div><div>It is not surprising that you do not find exactly the same CV values in the *-COLVAR.metadynLog.</div><div>The FES generated by graph is reconstructed from the metadynamics potential, made of Gaussian contributions centred on the points where the trajectory is found when the Gaussian is spawn. </div><div><br></div><div>The second issue is related to an error in reading the input.</div><div><br></div><div>Regards</div><div>Marcella</div><div><br></div><div><br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Tuesday, November 2, 2021 at 3:48:01 AM UTC+1 <a rel="nofollow">hujin...@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"><div>Dear cp2k users and developers</div><div><br></div><div>I'm learning the metadynamic recently and met the following problems about postprocessing.<br></div><div><br></div><div>The first one is that in the postprocessing of constructing the free energy surface, I used 'graph.popt -ndim 2 -ndw 1 2 -file *.restart -find-minima -cp2k' to get the minimum point on the free energy surface. I got three sets of data which include two CV values ​​and corresponding free energy values, respectively. But awkwardly, I cannot find the corresponding
CV value in the original *-COLVAR.metadynLog file and thus fail to find the specific
structural configuration
. So, I want to know how to find the structural configurationÂ
corresponding
to the minimum point on the free energy surface.</div><div><br></div><div>The second question is that I tried to use 'graph.popt -ndim 2 -ndw 1 2 -file *.restart -find path -point-a CVs -point-b CVs -cp2k' to get the path between the minimums, but the command lines went wrong as follows:</div><div><br></div><div>
forrtl: severe (59): list-directed I/O syntax error, unit -5, file Internal List-Directed Read<br>
Image          PC          Routine        Line      Source        <br>
graph.popt      00000000004F55FB  Unknown          Unknown  Unknown<br>
graph.popt      000000000051C5B1  Unknown          Unknown  Unknown<br>
graph.popt      000000000051B2D5  Unknown          Unknown  Unknown<br>
graph.popt      000000000040E935  MAIN__              330  graph.F<br>
graph.popt      000000000040CA62  Unknown          Unknown  Unknown<br>
<a href="http://libc-2.17.so" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=http://libc-2.17.so&source=gmail&ust=1636012241463000&usg=AFQjCNEz1rDlcbBOCSXaYDY2l_h3G3P2cQ">libc-2.17.so</a>    00002B42666F4555  __libc_start_main    Unknown  Unknown<br>
graph.popt      000000000040C969  Unknown          Unknown  Unknow</div><div><br></div><div>I have no idea about this problem. If someone can offer some help on any question between these two, I would be really appreciate!<br></div><div><br></div><div>Regards!</div><div>JHu<br></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div></blockquote></div>
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