[CP2K-user] [CP2K:16905] How to find the global minimum...?
Sam Broderick
waveman68 at gmail.com
Fri Apr 29 13:02:58 UTC 2022
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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>
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