[CP2K-user] [CP2K:18062] starting a AI MD simulation from minimised structure

[Niharendu Choudhury]

First of all, how big (no. of atoms) is your system?

If it is fairly small (around 500 -700 atoms with some 80 processors) then 
you can try to attempt AIMD simulation.

Best thing, I found, to start an AIMD simulation is to run a few pico 
seconds (may be 100-200 ps) classical simulation with a reasonable force 
field.
Then start your AIMD from the last step configuration.

Best of luck.

N Choudhury

On Monday, November 21, 2022 at 2:17:54 PM UTC+5:30 jingli... at gmail.com 
wrote:

> Thank you for your useful comments, I am starting to think about returning 
> to namd/gromacs. But before
> I do it, I wanted to ask you what criteria do you use to find out whether 
> the system is equilibrated or not. 
> I found this page https://www.cp2k.org/howto:md?do=  From it, I 
> understood that by looking at the column
> "Cons Qty[a.u.]" from the .ener file, one could get the difference between 
> the maximum and minimum of the
> curve and divide it by the kinetic energy, for an equilibrated system this 
> ratio should be < 1% Maybe I didn't
> get the point? 
>
>
> El lunes, 21 de noviembre de 2022 a las 0:38:09 UTC+1, 
> dresear... at gmail.com escribió:
>
>> 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 <jingli... 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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>>

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