[CP2K-user] [CP2K:16168] Re: Problems with metadynamics postprocessing
Marcella Iannuzzi
marci.akira at gmail.com
Wed Nov 3 08:01:38 UTC 2021
Dear JHu
if you understand how the reconstruction of the FES works, you know that
the Gaussian contributions to the metadynamics potential have a certain
extension, hence they also contribute to parts of the CVs meatspace that do
not correspond to points visited by the metatrajectory, which is the one
reported in *-COLVAR.metadynLog. Moreover these Gaussian contributions sum
up, and if the matadynamics settings are not properly chosen they might
even produce misleading FES topographies. I cannot judge whether this is
your case, but for sure it is to be expected that the minima on the FES
are not exact points of the metatrajectory in *-COLVAR.metadynLog. If they
are in completely unexpected regions, far from those most frequently
visited by the trajectory, the metadynamics settings are most probably not
properly chosen.
The -opt-path option of graph requires as input a path file, not the Hills
file.
Regards
Marcella
On Wednesday, November 3, 2021 at 7:06:56 AM UTC+1 hujin... at gmail.com wrote:
>
> Dear Marcella
>
> Thanks and sorry to bother you again. I understand the fact that the FES
> generated by graph is reconstructed but the minima I got from graph which
> contain the CVs' values cannot be found in *-COLVAR.metadynLog. Is this
> situation normal?
>
> And I tried another command line "graph.popt -ndim 2 -ndw 1 2 -opt-path
> *HILLS.metadynLog -orac". And it still went wrong as follows:
>
> ABORT in metadyn_tools/graph.F:198 CPASSERT failed
> forrtl: error (76): Abort trap signal
>
> Image PC Routine Line
> Source
> graph.popt 0000000000500274 Unknown Unknown Unknown
> libpthread-2.17.s 00002B6FF116F630 Unknown Unknown Unknown
> libc-2.17.so 00002B6FF5641387 gsignal Unknown
> Unknown
> libc-2.17.so 00002B6FF5642A78 abort Unknown
> Unknown
> graph.popt 000000000044E345 base_hooks_mp_cp_ 78
> base_hooks.F
> graph.popt 000000000040D97E MAIN__ 198 graph.F
>
> graph.popt 000000000040CA62 Unknown Unknown Unknown
> libc-2.17.so 00002B6FF562D555 __libc_start_main Unknown
> Unknown
> graph.popt 000000000040C969 Unknown Unknown Unknown
> Aborted (core dumped)
>
> Maybe you can give me some advice about the graph usage. Thanks in advance!
>
> Regards
> JHu
>
> On Tuesday, November 2, 2021 at 10:05:10 PM UTC+8 Marcella Iannuzzi wrote:
>
>>
>> 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
>>>>>
>>>>
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/9a3e57be-15f9-497e-9534-334ee3af5edan%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20211103/600b266b/attachment.htm>
More information about the CP2K-user
mailing list