[CP2K-user] [CP2K:16180] Re: FES from Metadynamic simulation with three collective variables

['Václav Havel' via cp2k]

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
在2021年2月18日星期四 UTC+8 上午11:02:20<trann... at gmail.com> 写道：

> 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 trann... 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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