[CP2K-user] [CP2K:18351] How to find the global minimum...?

['rabdel' via cp2k]

Hi,
You can try with this 
approach: https://doi.org/10.1016/j.micromeso.2019.109885
Best regards,
Rabdel

El viernes, 29 de abril de 2022 a las 15:02:58 UTC+2, wave... at gmail.com 
escribió:

> Hi
>
> In researching global optimization, I stumbled on a reply be Ole Schütt, 
> who is the author of the SWARM part of CP2K. He suggested that the methods 
> are somewhat older and to look at ASE <https://wiki.fysik.dtu.dk/ase/>. I 
> think this is what I will look into.
>
> Cheers
> Sam
>
> On Friday, January 22, 2021 at 4:59:34 PM UTC+1 Monu Joy wrote:
>
>> Thanks, Fangyong for the suggestion.
>>
>> On Fri, Jan 15, 2021 at 10:01 PM Fangyong Yan <fyya... at gmail.com> wrote:
>>
>>> Hi, Monu,
>>>
>>> The difference energy is -6235.818 - (-6235.824) = 0.006 Hartree = 
>>> 15.753 kj/mol. 
>>>
>>> So if you use 800 K, the Boltzmann factor is: exp(-dE/R/T) = 
>>> exp(-15.753*1000/8.314/800) = 0.09, which means you would have a 
>>> probability of 0.09 to "jump" from the lower energy to higher energy, by 
>>> the help of heat. 
>>>
>>> So I think NVT at 800K, may be helpful for exploring the potential 
>>> energy surface, even within 10ps. 
>>>
>>> Regards,
>>>
>>> Fangyong
>>>
>>>
>>> On Fri, Jan 15, 2021 at 8:08 PM Monu Joy <monuj... at gmail.com> wrote:
>>>
>>>> Hi Lucas & Fangyong
>>>>
>>>> Thanks for the help. I have performed two cell-opt calculations of 
>>>> guest at host where the following total energies respectively represent the 
>>>> guest at the center of the MOF pore and near to the pore surface -6235.818 
>>>> and -6235.824. Do you guys think that this energy difference is 
>>>> reasonable...?
>>>>
>>>> Also, do you by chance have any reference that shows local minimum 
>>>> geometry modulate the property of a system more effectively...? 
>>>>
>>>> Thank you so much for your help!
>>>>
>>>> -Monu
>>>>
>>>>
>>>> On Wednesday, 13 January, 2021, 10:01:30 am GMT-5, Lucas Lodeiro <
>>>> eluni... at gmail.com> wrote: 
>>>>
>>>>
>>>> Hi Monu and Fangyong,
>>>>
>>>> I disagree a little bit with Fangyong because an AIMD calculation is 
>>>> not cheaper, and if the barriers between local minimas are high, you cannot 
>>>> see a structural change with the MD, at least in the scale time of ps. 
>>>> Firstly, I would try to optimize a couple of structures and measure the 
>>>> energy differences, this will give you a little insight about the barriers 
>>>> (the minimum energy for the barriers), If they are high, the AIMD probably 
>>>> cannot move from one local minima to another. If they are little, you can 
>>>> see the structural changes, but in this case, probably the global minima is 
>>>> not sufficient to modulate the properties of the system, and some other 
>>>> local minima have to be taken into account.
>>>> Other way is to generate with a script random positions of the molecule 
>>>> into the MOF and minimize them with a semiempirical formulation, as XTB (
>>>> https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/QS.html#METHOD), 
>>>> and rerun with the level of theory that you want just the low energy ones.
>>>>
>>>> Regards - Lucas Lodeiro
>>>>
>>>>
>>>> El mié, 13 ene 2021 a las 0:07, Fangyong Yan (<fyya... at gmail.com>) 
>>>> escribió:
>>>>
>>>> Hi, Monu,
>>>>
>>>> To explore the free energy surface better, you may need to start at a 
>>>> high temperature, and then annealing down to the room temperature. And for 
>>>> each temperature, you can plot the radial distribution function, for your 
>>>> guest molecule and your MOF atoms, for example, at 800 K, 700 K, ...., 
>>>> 300K. The reason starting at high temperature is that you can use heat to 
>>>> get your guest molecule out of the potentially trapped free energy minima, 
>>>> so you can explore the free energy minima more completely. 
>>>>
>>>> Regards,
>>>>
>>>> Fangyong
>>>>
>>>> On Tue, Jan 12, 2021 at 10:01 PM Fangyong Yan <fyya... at gmail.com> 
>>>> wrote:
>>>>
>>>> Hi, Monu,
>>>>
>>>> You can run a molecular dynamics simulation at room temperature, for 
>>>> several picosecond, and then you can plot the radial distribution function, 
>>>> between your guest molecule and the MOF, by doing this you would have a 
>>>> general picture of the free energy surface of your guest molecule in the 
>>>> MOF. Then based on the free energy minima structures, you can start to 
>>>> optimize your guest-MOF complex structure. (the free energy surface may be 
>>>> different from the potential energy surface, but at least by doing MD 
>>>> simulation and calculating the free energy surface based on radial 
>>>> distribution function, you can have a basic idea about the free energy 
>>>> surface, which should not be quite different from potential energy surface).
>>>>
>>>> Regards,
>>>>
>>>> Fangyong
>>>>
>>>> On Tue, Jan 12, 2021 at 7:20 PM Monu Joy <monuj... at gmail.com> wrote:
>>>>
>>>> Hi there
>>>>
>>>> I have a general question: I would like to find out the global minimum 
>>>> of a guest molecule within the pore of a MOF. I know I can place the guest 
>>>> molecule in the pore and get the host-guest structure optimized, but if I 
>>>> would place the guest molecule in another position of the same pore, there 
>>>> also I can get the structure optimized. In this scenario how could I find 
>>>> the exact most probable location of the guest molecule within the MOF pore 
>>>> or its global minimum...?
>>>>
>>>> Any help would be highly appreciated...
>>>>
>>>> -Monu
>>>>
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>>
>> -- 
>> *Thanks with Regards*
>>
>

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