[CP2K-user] [CP2K:21502] Re: PES plot

[Mawuli]

Hi all,
I generated a 3D free energy surface plot of my system. I observed an 
unexpected result: the simulation sampled an additional state that appears 
to be lower in energy than the reactant. This is surprising, as the 
reactant is expected to be the lower-energy species. 
Upon further inspection, this new state resembles the product of the 
reaction. However, based on the previous study—specifically the glucose 
ring-opening mechanism described in DOI: 10.1021/jp402739q—the product 
should be higher in energy than the reactant. 

I would appreciate any insights into why this lower-energy product-like 
state might be appearing in the simulation, or if this could indicate an 
alternative reaction pathway or artifact in the sampling.

Thank you.
Mawuli


On Wednesday, May 21, 2025 at 12:16:00 PM UTC-4 mawuli deegbey wrote:

> Great and thank you for the explanation. 
>
> Mawuli 
>
> On Wed, May 21, 2025 at 11:29 AM Marcella Iannuzzi <marci... at gmail.com> 
> wrote:
>
>> Hi Mawuli
>>
>> It is exactly thanks to the accumulation of additional sampling that the 
>> shape  of the FES changes. 
>> This is the scope of metadynamics. I do not see anything strange in the 
>> plots, actually it seems to  work pretty well.
>>
>> Regards
>> Marcella
>>
>> On Wednesday, May 21, 2025 at 5:17:44 PM UTC+2 Mawuli wrote:
>>
>>> Hi Marcella,
>>>
>>> My goal is to analyze the convergence of my simulations.  
>>> I’m trying to figure out why the free energy surface in dataset 11 shows 
>>> a higher energy well compared to datasets 9 and 10, despite being a 
>>> continuation, and if such cases do occur.
>>>
>>> Yes, I restarted the metadynamics simulations to collect additional 
>>> data. 
>>>
>>> Thank you.
>>> Mawuli
>>>
>>> On Wednesday, May 21, 2025 at 4:26:06 AM UTC-4 Marcella Iannuzzi wrote:
>>>
>>>> Hi ...
>>>> I am not sure of understanding your question correctly. 
>>>> If you are restarting metadynamics and collecting more data, the 
>>>> earlier sampling was simply not converged yet. 
>>>> Regards
>>>> Marcella
>>>>
>>>> On Wednesday, May 21, 2025 at 9:05:51 AM UTC+2 Mawuli wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Could someone please help me figure out why my well-tempered 
>>>>> metadynamics sampled a higher energy well after sampling a lower one? 
>>>>> For instance, within the range of 0.5 to 1.0, Data 11 (purple color) 
>>>>> shows a higher energy than Data 8 to Data 10. After another sampling, a 
>>>>> lower energy is obtained for Data 12. 
>>>>>
>>>>> I generated all these data points (fes.dat) using the CP2K graph tool. 
>>>>>
>>>>> Thank you.
>>>>>
>>>>>
>>>>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "cp2k" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to cp2k+uns... at googlegroups.com.
>> To view this discussion visit 
>> https://groups.google.com/d/msgid/cp2k/8e3b3558-0f75-4ac1-b532-6878a664014cn%40googlegroups.com 
>> <https://groups.google.com/d/msgid/cp2k/8e3b3558-0f75-4ac1-b532-6878a664014cn%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>

-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/cp2k/0306509c-1fed-407a-89d0-3840c829ae50n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20250528/a06db839/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 3D_plot.png
Type: image/png
Size: 5362598 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20250528/a06db839/attachment-0001.png>