[CP2K-user] [CP2K:16161] Re: Problems with metadynamics postprocessing
Marcella Iannuzzi
marci.akira at gmail.com
Tue Nov 2 14:05:10 UTC 2021
Dear JHu
Each minimum on the FES corresponds to specific values of the CVs, as you
defined them. Hence, any structure for which the CVs take those values
belongs to the minimum. There is no one specific set of coordinates.
I expect that the points among which the path is calculated should be taken
from the generated FES and not from the restart file.
Kind regards
Marcella
On Tuesday, November 2, 2021 at 2:13:34 PM UTC+1 hujin... at gmail.com wrote:
>
> Dear Marcella
>
> Really thanks for your reply. So, as for the first problem, do you know
> how to locate the exact minimum of FE and find the corresponding structure?
> Sorry that I have no idea about it.
>
> As for the second, since the FES is reconstructed, the data of "-point-a"
> should belong to the *.restart file rather than the values I got from the
> first step 'graph.popt -ndim 2 -ndw 1 2 -file *.restart -find-minima -cp2k'
> , right?
>
> Regards
> JHu
>
> On Tuesday, November 2, 2021 at 4:35:49 PM UTC+8 Marcella Iannuzzi wrote:
>
>>
>> Dear JHu
>>
>> It is not surprising that you do not find exactly the same CV values in
>> the *-COLVAR.metadynLog.
>> The FES generated by graph is reconstructed from the metadynamics
>> potential, made of Gaussian contributions centred on the points where the
>> trajectory is found when the Gaussian is spawn.
>>
>> The second issue is related to an error in reading the input.
>>
>> Regards
>> Marcella
>>
>>
>>
>> On Tuesday, November 2, 2021 at 3:48:01 AM UTC+1 hujin... at gmail.com
>> wrote:
>>
>>> Dear cp2k users and developers
>>>
>>> I'm learning the metadynamic recently and met the following problems
>>> about postprocessing.
>>>
>>> The first one is that in the postprocessing of constructing the free
>>> energy surface, I used 'graph.popt -ndim 2 -ndw 1 2 -file *.restart
>>> -find-minima -cp2k' to get the minimum point on the free energy surface. I
>>> got three sets of data which include two CV values and corresponding
>>> free energy values, respectively. But awkwardly, I cannot find the
>>> corresponding CV value in the original *-COLVAR.metadynLog file and thus
>>> fail to find the specific structural configuration . So, I want to know how
>>> to find the structural configuration corresponding to the minimum point on
>>> the free energy surface.
>>>
>>> The second question is that I tried to use 'graph.popt -ndim 2 -ndw 1 2
>>> -file *.restart -find path -point-a CVs -point-b CVs -cp2k' to get the path
>>> between the minimums, but the command lines went wrong as follows:
>>>
>>> forrtl: severe (59): list-directed I/O syntax error, unit -5, file
>>> Internal List-Directed Read
>>> Image PC Routine Line
>>> Source
>>> graph.popt 00000000004F55FB Unknown
>>> Unknown Unknown
>>> graph.popt 000000000051C5B1 Unknown
>>> Unknown Unknown
>>> graph.popt 000000000051B2D5 Unknown
>>> Unknown Unknown
>>> graph.popt 000000000040E935 MAIN__
>>> 330 graph.F
>>> graph.popt 000000000040CA62 Unknown
>>> Unknown Unknown
>>> libc-2.17.so 00002B42666F4555 __libc_start_main
>>> Unknown Unknown
>>> graph.popt 000000000040C969 Unknown
>>> Unknown Unknow
>>>
>>> I have no idea about this problem. If someone can offer some help on any
>>> question between these two, I would be really appreciate!
>>>
>>> Regards!
>>> JHu
>>>
>>
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