[CP2K-user] [CP2K:18061] starting a AI MD simulation from minimised structure

[jing liang]

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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