[CP2K-user] [CP2K:17083] Re: graph.popt tool for metadynamics

[Marcella Iannuzzi]

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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