[CP2K-user] [CP2K:18577] Re: Problems about doing metadynamics of CO2 adsorption

[Marcella Iannuzzi]

Dear Yibo Wang, 

I cannot say whether the simulation is reasonable now. 
If the initial forces obtained from a not converged electronic structure 
calculation are very wrong, it is possible that the system ended up in an 
unphysical structure from which it will never come back. Or maybe not.
Anyway, it would be for sure much better to run a stable MD with your new 
system, before running metadynamics.
It is indeed very important to monitor the sampling of the configurational 
space with an unbiased dynamics to be able to define useful collective 
variables and to set the reasonable parameters. 
In addition to that, I strongly suggest to also read review papers on 
metadynamics before starting using it, such that you can decide which type 
of approach is best suitable for your system.
For instance the lambda and mass parameters are only needed for a 
lagrangian metadynamics. Are you sure that you are using this option? And 
if yes, are you sure that this is the optimal choice for your needs?
You also have a wall in your definition. How can you set it before knowing 
which is the unbiased behaviour of the collective variable?

Unfortunately metadynamics, as most of the methods in molecular 
simulations, is not just a black box tool, you need to know very well what 
you are doing to  avoid generating unreliable results. 

Regards,
Marcella




On Wednesday, March 22, 2023 at 9:50:02 AM UTC+1 yibowang333 wrote:

> Dear Marcella 
>
> First of all thanks a lot for your help.
>
> The water molecules in the system are copied directly from a previous aimd 
> simulation that has been balanced. I just replaced the metal atoms 
> supported in the previous C2N graphene. This may lead to its unreasonable 
> initial structure and slow convergence. In fact ,the trajectory file 
> actually started output after I sent the email shortly. However, there is a 
> reminder "WARNING in qs_scf.F:598 :: SCF run NOT converged" in the output 
> file , but the subsequent SCF operations have converged (Sometimes I also 
> encounter this situation when doing geometry optimization). Are the results 
> credible in this case?
>
> In addition, I also think that the slow operation may be caused by the 
> unreasonable parameter setting in the input file. I don't quite understand 
> the meaning of the keywords LAMBDA and MASS under the METAVAR scetion. I 
> just learned from your lecture on YouTube that their unit changes with the 
> unit of CV.I don't know their specific impacts of the system while doing 
> metadynamics(maybe of my poor English listening?). I want to know if it is 
> reasonable to set such a setting with reference to the parameters in your 
> course ppt.
>         &METAVAR
>            COLVAR 1
>            SCALE 0.2
>            LAMBDA 0.8
>            MASS 20 
>           &WALL 
>             POSITION 5.0
>             TYPE QUADRATIC 
>               &QUADRATIC 
>                 DIRECTION WALL_MINUS
>                 K 0.5
>               &END QUADRATIC 
>            &END WALL
>          &END METAVAR
>
>
> Appreciate again for your help!
>
> Sincerely,
> Yibo Wang
>
> yibowang333
> yibow... at gmail.com
>
> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=yibowang333&uid=yibowang333%40gmail.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=%5B%22yibowang333%40gmail.com%22%5D> 
> ---- Replied Message ---- 
> From Marcella Iannuzzi<marci... at gmail.com> 
> Date 3/22/2023 15:36 
> To cp2k<cp... at googlegroups.com> 
> Subject [CP2K:18575] Re: Problems about doing metadynamics of CO2 
> adsorption 
> Dear Yibo Wang
>
> If there is no MD output most probably the electronic structure 
> optimization at the very first step is not converging. 
> If this is the case, one should first work on the electronic structure 
> settings.
> Could you run ab initio MD without metadynamics for the same system?
>
> Regards
> Marcella
>
> On Wednesday, March 22, 2023 at 2:29:43 AM UTC+1 yibowang333 wrote:
>
>> Dear users and developers,
>>     
>>     I want to do a metadynamic test of CO2 adsorption on a C2N graphene, 
>> but I found that there is still no output trajectory file after running for 
>> nearly 15 hours. I chose the distance from an O atom(in red color) and C 
>> atom(in gray color) in the CO2 molecule to the Fe atom(in green color) on 
>> the substrate as the CV.  I think this setting should be reasonable. I 
>> wrote the following input file with reference to the ppt on the official 
>> course, but I don't know if it is accurate. In addition, I don't quite 
>> understand the meaning of the parameters in lambda, mass and WALL in the 
>> metavar module. I hope I can get an explanation if possible. Below is my input 
>> file,the initial structure,  and the final state I want to have.
>>
>>     Appreciate a lot for your help!
>>
>> Sincerely,
>> Yibo Wang
>>
>> yibowang333
>> yibow... at gmail.com
>>
>> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=yibowang333&uid=yibowang333%40gmail.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=%5B%22yibowang333%40gmail.com%22%5D> 
>>
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