[CP2K-user] [CP2K:14565] How to find the global minimum...?

[Monu Joy]

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
>>
>> --
>> 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 cp... at googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/cp2k/1852672747.3320.1610497192914%40mail.yahoo.com
>> <https://groups.google.com/d/msgid/cp2k/1852672747.3320.1610497192914%40mail.yahoo.com?utm_medium=email&utm_source=footer>
>> .
>>
>> --
>> 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 cp... at googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/cp2k/CAJjmc%2BKviWAFmj5UmYqMWL1Z5wFpQZjdKkhGS%2B7CTp7-6jaLgg%40mail.gmail.com
>> <https://groups.google.com/d/msgid/cp2k/CAJjmc%2BKviWAFmj5UmYqMWL1Z5wFpQZjdKkhGS%2B7CTp7-6jaLgg%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>>
>> --
>> 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 cp... at googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/cp2k/CAOFT4PKCKjc0vOGZUkbjsDEEqJM_w_UxYK-PC%2Bt-vnzZzLhrgg%40mail.gmail.com
>> <https://groups.google.com/d/msgid/cp2k/CAOFT4PKCKjc0vOGZUkbjsDEEqJM_w_UxYK-PC%2Bt-vnzZzLhrgg%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>>
>> --
>> 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 cp... at googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/cp2k/1361749041.8962.1610759305502%40mail.yahoo.com
>> <https://groups.google.com/d/msgid/cp2k/1361749041.8962.1610759305502%40mail.yahoo.com?utm_medium=email&utm_source=footer>
>> .
>>
> --
> 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 cp... at googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/CAJjmc%2BKyP-zV-p%2B%2BZtUkTgqoWQnovqnUvaVpG7NQby7a8KURgQ%40mail.gmail.com
> <https://groups.google.com/d/msgid/cp2k/CAJjmc%2BKyP-zV-p%2B%2BZtUkTgqoWQnovqnUvaVpG7NQby7a8KURgQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>


-- 
*Thanks with Regards* <monupl... at yahoo.com>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20210122/f5e64c0b/attachment.htm>