Problems with minimum energy pathways calculated by the graph.popt tool.

René Schliemann rjat... at
Tue Jun 26 12:25:09 UTC 2018

Hi again,

so due to the lack of answers I would like to rephrase my question and hope 
someone might know the answer.
The setup for the CVs is the same like mentioned above. I found out, that 
if I plot the summed up FES (with VISIT) processed by the 
graph utility I see completely different energy values for the minima than 
the ones optained with the -find-minima option.

So my new question is, how do I use the graph.popt correctly to gain 
information about minima on the FES and minimum energy pathways between 
I really appreciate your help.

Best regards,
René Schliemann

Am Dienstag, 17. April 2018 11:23:00 UTC+2 schrieb René Schliemann:
> Hello,
> I would like to ask for help concerning the post processing module for 
> metadynamic simulations included in the CP2K code graph.popt.
> I am investigating dissolution processes at the mineral surfaces in water. 
> So far I did some metadynamics calculations with cp2k using three 
> collective variables (CVs), each of which are coordination numbers of one 
> specific atom at the surface towards surrounding species on the surface 
> and OH-groups. 
> Now the one thing I am wondering about is the following: 
> With graph.popt module I obtain the FES and respective minima like this:
> *graph.popt -ndim 3 -ndw 1 2 3 -periodic 1 2 3 -file *-1.restart 
> -find-minima -cp2k *
> Then I sort the minima by free energy value, from lowest to highest. 
> After sorting them I search for two minima having specific CV 
> combinations, one being close to the configuration at the start of the 
> simulation
> (tolerance of up to 0.2) and the second is the CV configuration where the 
> coordination number to surrounding species at the surface becomes
> close to zero (again 0.2 tolerance), which means it is dissolved. With the 
> found CV points from the minima file I run the following:
> *graph.popt -ndim 3 -ndw 1 2 3 -periodic 1 2 3 -file *-1.restart 
> -find-path -point-a CV1(start) CV2(start) CV3(start) -point-b CV1(diss) 
> CV2(diss) CV3(diss) -cp2k*
> What I don’t quite understand is now in the file the path 
> sometimes go through a point which is lower in free energy than the global
> minimum found by the minima search. How is this possible, can I somehow 
> correct for this or do I have to change sth. in the CV setup?
> If you need anymore insight or maybe some files just tell me.
> I would appreciate your help. Thank you in advance.
> Best regards,
> René Schliemann
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the CP2K-user mailing list