FES from Metadynamic simulation with three collective variables

[Nam Tran]

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

[Marcella Iannuzzi]

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 

[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

[Václav Havel]

Dear Nam

I run the command "graph.popt -ndim 3 -ndw 1 2 3 -file metad.restart -find-path -point-a CVs(point A) -point-b CVs(point B) -cp2k", But get errors :

forrtl: severe (59): list-directed I/O syntax error, unit -5, file Internal List-Directed Read

Image              PC                Routine            Line        Source             

graph.popt         00000000004584DE  for__io_return        Unknown  Unknown

graph.popt         000000000047B6ED  for_read_int_lis_     Unknown  Unknown

graph.popt         0000000000479E56  for_read_int_lis      Unknown  Unknown

graph.popt         000000000040B740  Unknown               Unknown  Unknown

graph.popt         00000000004B4CD2  Unknown               Unknown  Unknown

libc-2.17.so       00002B5BED02C555  __libc_start_main     Unknown  Unknown

graph.popt         0000000000409729  Unknown               Unknown  Unknown

Do you know why? 

Thanks advance

Best

Vaclav