[CP2K-user] [CP2K:17084] Re: graph.popt tool for metadynamics

Laura Bonometti laura.bonometti at edu.unito.it
Mon Jun 6 08:17:34 UTC 2022

Dear Marcella,

Thank you for your help!
I attach here the restart file used for obtaining the FES from graph.popt 
if this can help.
For running the calculation with graph.popt I wrote: graph.popt -cp2k -ndim 
2 -ndw 1 2 -file metadyn_Ni_6Li_new-1_59500.restart -out fes.dat .
Do I have to add some other information?
Maybe I let the calculation run for too long, depositing too much 
Gaussians, so maybe I have to stop the calculation/consider another restart 
file related to a lower number of computed steps, obviously considering 
that the particle reached the expected position. 


Il giorno lunedì 6 giugno 2022 alle 09:46:00 UTC+2 Marcella Iannuzzi ha 

> Dear Laura,
> Difficult to guess what is going wrong with graph.popt. Maybe there is 
> some normalisation factor that is wrongly set for the calculation of a 
> multi-dimensional FES.
> Maybe more information would help.
> The python script you are indicating, though, it is not generating a FES 
> from a metadynamics  potential. It builds a probability histogram from a 
> standard molecular dynamics sampling.
> This cannot be directly applied to an enhanced sampling, because you are 
> not taking into account the bias potential in collecting the probability 
> distribution. 
> Regards
> Marcella
> On Friday, June 3, 2022 at 6:51:17 PM UTC+2 laura.b... at edu.unito.it wrote:
>> Hi everyone!
>> I am using CP2K for running metadynamics simulations. I used the 
>> graph.popt tool for obtaining the free energy of my system, but actually I 
>> can't understand how it is calculated. I read that the final energy results 
>> are in hartree but if I convert them in eV they do not make any sense in 
>> terms of order of magnitude, even if the obtained curve is in agreement 
>> with what I expected. I know that the free energy should be calculated 
>> considering the probability distribution of the CVs but if I try to 
>> reconstruct the curve in this way, I don't obtain the same results obtained 
>> by exploiting the graph.popt tool. I also tried to use the python script 
>> found at  https://www.cp2k.org/exercises:2021_uzh_acpc2:ex03 and the 
>> range of free energy is reasonable in this case, but completely different 
>> respect to what obtained by using graph.popt, so I think that I'm not 
>> understanding what is printed by this program.
>> Can you help me to solve this question?
>> Kind regards,
>> Laura

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