[CP2K-user] [CP2K:18016] Re: Problems optimising a heme (Fe2+) group

[Sara Llap]

Dear Marcella,

Thank you for your help. It took me a lot of attempts but I managed to
converge the calculation.

Thank you again!

Sara

El jue, 22 sept 2022 a las 9:39, Marcella Iannuzzi (<marci.akira at gmail.com>)
escribió:

>
>
> Dear Sara
>
> Starting around step 50 the coordinates do not change anymore
> Max. step size             =         0.0000000000
> The gradient  above tolerance is only one. It is the x component of the
> force on atom 47, a hydrogen.
> It remains practically constant for many steps.
> It seems that the optimisation algorithm is not in the conditions of
> performing any CG step, and the SD gets stuck.
> So since step 50 nothing changes in the structure.
> I would try and change the optimiser to BFGS.
>
> Kind regards
> Marcella
>
>
> On Wednesday, September 21, 2022 at 11:30:55 PM UTC+2 salla... at gmail.com
> wrote:
>
>> Dear Ivan, Victor and Marcella,
>>
>> Thank you so much for your help.
>>
>> I have been reading the bibliography you suggested and using your inputs
>> and I almost optimised the heme group. I got to a point where the
>> optimisation does not seem to converge but it is really close.
>>
>> --------  Informations at step =   114 ------------
>>
>>   Optimization Method        =                   SD
>>
>>   Total Energy               =      -517.5364879764
>>
>>   Real energy change         =         0.0000000050
>>
>>   Decrease in energy         =                   NO
>>
>>   Used time                  =              460.425
>>
>>
>>   Convergence check :
>>
>>   Max. step size             =         0.0000000000
>>
>>   Conv. limit for step size  =         0.0010000000
>>
>>   Convergence in step size   =                  YES
>>
>>   RMS step size              =         0.0000000000
>>
>>   Conv. limit for RMS step   =         0.0010000000
>>
>>   Convergence in RMS step    =                  YES
>>
>>   Max. gradient              =         0.0012644252
>>
>>   Conv. limit for gradients  =         0.0010000000
>>
>>   Conv. for gradients        =                   NO
>>
>>   RMS gradient               =         0.0002927175
>>
>>   Conv. limit for RMS grad.  =         0.0010000000
>>
>>   Conv. in RMS gradients     =                  YES
>>
>>  ---------------------------------------------------
>>
>>
>> I have been playing a bit with the parameters but I haven't managed to
>> make it work.
>>
>>
>> Thanks again,
>>
>> Kind regards,
>>
>>
>> Sara
>>
>> El jue, 15 sept 2022 a las 17:57, Marcella Iannuzzi (<marci... at gmail.com>)
>> escribió:
>>
>>> Dear Sara
>>>
>>> Before starting a geometry optimisation it is  good practice to get a
>>> converged single point calculation.
>>> If I understand correctly from the output you posted, this was not the
>>> case.
>>>
>>> I played a bit with the settings for your system and I got a converged
>>> single point calculation at the PBE level of theory
>>> for the molecule charged --2 (see the attached file).
>>>
>>> Kind regards
>>> Marcella
>>>
>>> On Tuesday, September 13, 2022 at 4:00:25 PM UTC+2 salla... at gmail.com
>>> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I am having problems on a geometry optimisation of a heme group with
>>>> Fe2+ using PBE in CP2K. My calculations run and the total energy is
>>>> decreasing. However, the job has been running for almost a month and it
>>>> doesn't seem to converge.
>>>>
>>>> I am not an expert on CP2K nor on transition metals. I would really
>>>> appreciate it if you could help me sort this out. I have  attached the
>>>> restart file and the output for clarity.
>>>>
>>>> Thanks a lot,
>>>>
>>>>
>>>> Sara
>>>>
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