[CP2K-user] [CP2K:14563] How to find the global minimum...?

[Fangyong Yan]

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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