[CP2K-user] [CP2K:18059] starting a AI MD simulation from minimised structure

[DMITRII Drugov]

Ideally you need to use force field to optimize your structure classically.
I do this for liquids.
Then, you can continue NVE, T by quick step CP2K. Equilibration with AibMD
is very time consuming, you will unlikely be able to equilibrate random
structure with >300-500 atoms, or you could but it will be very expensive
and long simulation. I couldn't equilibrate NPT of random liquid of
16*31+32*18+32 atoms with 36-48 cores for more than a month.





On Mon, Nov 21, 2022, 1:18 AM jing liang <jingliang2015 at gmail.com> wrote:

> I am trying to see how the structure evolves in time, and monitor where
> some bond rotation occurs. The long story short, I
> could pack all relevant molecules in a box. I was doing some search for
> parameters for gromacs/namd/... but I found it
> not straightforward, also the mixing of force fields is something I am not
> completely sure about. Then, I thought that pure
> CP2K simulation could work, and it is doing a great deal in the
> minimisation process. But I don't know how long it could
> take to converge completely.
>
> As I wrote before, the goal of this simulation would be to see if some
> bond rotation occurs in the long term some spectra
> would be great but at this point just the dynamics. That's why I asked
> here if there is some standard/accepted criteria
> for using a structure as the initial frame for an AI MD simulation
> regarding the energies/forces. Thanks for you comments.
>
>
>
> El domingo, 20 de noviembre de 2022 a las 15:40:11 UTC+1,
> dresear... at gmail.com escribió:
>
>> This is a good question but it depends on what you are simulating. If it
>> is non- equilibrium system then it is pointless to look at the energy,
>> temperature, pressure etc.
>>
>> If it is equilibrium system, it should be similar to classical MD but on
>> a shorter time scale. There is a tutorial how to calculate IR spectra with
>> cp2k, you can find steps there for equilibration and spectrum data
>> acquisition.
>> It is on cp2k website.
>>
>>
>> On Sun, Nov 20, 2022, 5:33 PM jing liang <jingli... at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I created a simulation box manually and then started a minimisation
>>> process
>>> by using geometry optimisation. My goal is not to get a fully optimised
>>> structure
>>> but to start a MD simulation using the NVE ensemble. My question is if
>>> one needs
>>> a fully optimised structure in order to start MD or if there is a
>>> criterion to say
>>> that the minimised structure is already fine?
>>>
>>> I am coming from classic MD simulations where some software suggest to
>>> have
>>> the forces converged up to some particular threshold.
>>>
>>> Thanks
>>>
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