<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 2
-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<br>Image PC Routine Line Source <br>graph.popt 0000000000500274 Unknown Unknown Unknown<br>libpthread-2.17.s 00002B6FF116F630 Unknown Unknown Unknown<br>libc-2.17.so 00002B6FF5641387 gsignal Unknown Unknown<br>libc-2.17.so 00002B6FF5642A78 abort Unknown Unknown<br>graph.popt 000000000044E345 base_hooks_mp_cp_ 78 base_hooks.F<br>graph.popt 000000000040D97E MAIN__ 198 graph.F<br>graph.popt 000000000040CA62 Unknown Unknown Unknown<br>libc-2.17.so 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 href data-email-masked 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 configuration
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=1635993825461000&usg=AFQjCNEOnweiwnHHNPtRT9Ba8yxkQaB0XQ">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>
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