[CP2K-user] [CP2K:17911] Re: Molecules moving far apart during metadynamics

[Aditya Goyal]

Dear Marcella
Thanks for your reply. I did apply WALL  associated with collective 
variables (coordination numbers of C  and O in parent molecule) for my 
system. I applied a lower limit (found using an unbiased MD run) of 
coordination numbers using WALL_MINUS.
But the water molecule was still moving away inside the system during 
metaD. run, probably because the system could still maintain the wall limit 
with/without water.  Could you please suggest any different way to apply 
WALLS for this system? Also, you suggested using an external potential 
confining the coordinates within a certain region of space. Could you 
please explain the keywords of CP2K  to apply external potential for any 
system? 

Regards
Aditya

On Wednesday, October 19, 2022 at 2:35:04 PM UTC+5:30 Marcella Iannuzzi 
wrote:

> Dear Aditya
>
> You can use either a WALL associated to some collective variable, or an 
> external potential confining the coordinates within a certain region of 
> space. 
> Regards
> Marcella
>
> On Tuesday, October 18, 2022 at 2:56:02 PM UTC+2 goyal.a... at gmail.com 
> wrote:
>
>> On Tuesday, October 11, 2022 at 9:24:13 PM UTC+5:30 mattwa... at gmail.com 
>> wrote:
>>
>>> Hello,
>>> sorry I don't know the metadynamics code well.
>>> Maybe if you explain very clearly what you want to achieve and include 
>>> your input / output you can get more assistance.
>>> Matt
>>>
>>> On Thursday, 6 October 2022 at 14:41:14 UTC+1 goyal.a... at gmail.com 
>>> wrote:
>>>
>>>> Dear All,
>>>>
>>>> I am performing metadynamics simulation on my system having 2 molecules 
>>>> to perform a reaction with coordination numbers as 2 collective variables. 
>>>> Unfortunately, a molecule is moving far apart from the other molecule 
>>>> (fixed) during simulation. So, I wanted to apply a boundary to restrict the 
>>>> motion of moving molecule within a certain distance (d) from the fixed 
>>>> molecule,  to maintain enough interactions to perform this reaction. I've 
>>>> seen some answers suggesting restraining the distance using a collective 
>>>> variable but that would fix the moving molecule to distance 'd '  in space 
>>>> and restrict its motion for distances ≤ d .  Ideally, the moving molecule 
>>>> should stay within distance : (0 to d ) for a good metadynamics run. Any 
>>>> suggestions would be appreciated.  
>>>>
>>>> Regards
>>>>
>>>> Aditya
>>>>
>>>

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