[CP2K-user] FES from Metadynamic simulation with three collective variables

[Nam Tran]

Dear Prof. Marcella

Thank you for your quick reply. Your reference is very helpful.

I just realized that, the *graph.popt* module could be used to scan the 
minima in the whole FES.
*graph.popt -ndim 3 -ndw 1 2 3 -file metad.restart -find-minima -cp2k*
Then the MEP connecting two selected minima can be calculated using the 
same module. 
*graph.popt -ndim 3 -ndw 1 2 3 -file metad.restart -find-path -point-a 
CVs(point A) -point-b CVs(point B) -cp2k*

Best regards
Nam
On Tuesday, 16 February 2021 at 7:46:29 pm UTC+11 Marcella Iannuzzi wrote:

> Dear Nam,
>
> The FES can be integrated in some directions in order to reduce the 
> dimensionality  and to be able to plot a profile or a contour along one or 
> two coordinates only. 
> Obviously information along the integrated out coordinates will be lost. 
> As alternative, one can find  minimum energy pathways connecting given 
> points scanning the whole FES
> The resulting pathway is a function of all  CVs.
>
> The method works in principle with any number of CVs, 
> but   increasing the number of CVs makes the time required for exploring 
> the  FES longer and the interpretation of the results more difficult. 
>
> You can find in the literature discussions on how to analyse the CVs space.
> An example in https://doi.org/10.1063/1.5027528
>
> Regards
> Marcella 
>
> On Monday, February 15, 2021 at 3:32:38 PM UTC+1 tr... at gmail.com wrote:
>
>> Hi,
>>
>> I have done a metadynamics calculation with cp2k using two collective 
>> variables (CVs). It is very intuitive in this case to plot the contour of 
>> the free energy corresponding to the two collective variable. From the 
>> contour plot I can easily define the minima and the MEP between them. I can 
>> also calculate the barrier energy from the MEP.
>>
>> Now I want to do a simulation with three collective variable. Is there 
>> any easy way to find the minima as well as MEP between those minima?. I 
>> found it has been done in the ref: 
>> https://pubs.acs.org/doi/10.1021/acscatal.9b00239, but I don't know how.
>> Also, If I want to increase the number of CVs i.e., into 4 or 5. Does the 
>> method still work?
>>
>> Best regards
>> Nam
>>
>
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