[CP2K-user] [CP2K:20984] Re: Problems of setting collective variables in constrained AIMD simulation

[jiawei ge]

Hello, have the problems you met solved? I also met it. 

On Friday, June 21, 2024 at 4:41:37 PM UTC+8 Bai Li wrote:

> Dear CP2K Users,
>
> I am attempting to perform constrained AIMD simulations using CP2K to 
> study the solvation process of a diatomic molecule (X2) transitioning from 
> the gas phase to a solvent model represented by a slab water model. In the 
> constrained AIMD simulation, I define a collective variable (CV) as the 
> distance between the geometry center of X2 and the geometry center of all 
> water molecules in the water slab. I fixed this CV and performed dynamics 
> simulations at 300 K. 
>
> However, in the final simulation results (taking CV = 9.0 Å as an 
> example), some water molecules escape beyond the cell boundaries defined in 
> my input file. To address this, I applied a wrapping operation to the 
> atomic/molecular positions in the output pos.xyz file, bringing the 
> out-of-cell atoms/molecules back into the cell using periodic boundary 
> conditions. Then, I recalculated the CV for each image in the trajectory. 
> Surprisingly, after wrapping all atoms/molecules periodically, the CV is no 
> longer the initial value (9.0 Å), but instead takes on different values. 
> However, if I skip the wrapping operation, the CV remains at the initial 
> value of 9.0 Å. It seems that the CV definition does not account for 
> periodicity during the simulation. 
>
> I would like to ask whether CP2K has this issue, or if there might be 
> other reasons causing this problem in my simulation results.
>
> If someone have time to give me some advice, I would appreciate it.
>
> Best regards
>

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