CP2K tutorial for biochemical systems

Dries Van Rompaey dries.va... at gmail.com
Wed Jul 19 15:40:39 CEST 2017


Hi,

You can observe the reaction occurring by visualising the xyz files of 
metadynamics qmmm simulation - you will see the C-O bond breaking and the 
C-C bond forming. You can also plot the collective variable in the 
metadynlog file: the 3 to 8 bohr region is occupied by the substrate and 
the -3 to -8 region is occupied by the product.

Hope this helps,

Dries

Op woensdag 19 juli 2017 15:12:14 UTC+2 schreef jts2... at gmail.com:
>
> Thanks for your reply, Dries !
>
> The first paragraph you said is understood. I also wonder how does one 
> know the reaction really occurs in the simulation ? i.e. Which part of the 
> output file is important to know the information about the reaction ?
>
> I major in  calculation mathematics, therefore the easy thing for you may 
> seems hard for me.
> I'll appreciate for your reply !
>
>
>
> 在 2017年7月19日星期三 UTC+8下午8:00:59,Dries Van Rompaey写道:
>>
>> Hi,
>>
>> The MM simulations in the tutorial are intended to allow the system to 
>> relax and to find suitable cell dimensions. We do this at the MM level 
>> because it's rather fast when compared to QMMM. The relaxed system is then 
>> moved to the QMMM level in order to simulate bond breaking. 
>>
>> The reaction is not sampled in the *unbiased* QMMM, which is why we add 
>> metadynamics in the second part. Once we bias the collective variable, you 
>> can see the reaction occurring at the QMMM level.
>>
>>
>> Op woensdag 19 juli 2017 13:34:52 UTC+2 schreef jts2... at gmail.com:
>>>
>>> Hi Dries,
>>>
>>> I have read the tutorial and wonder how could I show the advantage of 
>>> QMMM calculation over MM calculation. Should I run a complete MM simulation 
>>> and compare the two results ? I notice that you said in the tutorial that 
>>> the reaction is not achieved in the simulation. Does that mean QMMM method 
>>> doesn't work in this simulation ? 
>>>
>>> 在 2017年7月18日星期二 UTC+8下午2:49:11,Dries Van Rompaey写道:
>>>>
>>>> Hi cp2k-users,
>>>>
>>>> After experimenting with cp2k for a while I have written down a short 
>>>> tutorial on how to use cp2k for biochemical systems. The tutorial covers 
>>>> the setup of an enzyme system with ambertools followed by equilibration 
>>>> with cp2k at the MM level, after which we move the system to QM/MM for 
>>>> metadynamics simulations of an enzymatic reaction. I am far from an expert 
>>>> myself, but I thought this might be useful to people starting out. If you 
>>>> spot any mistakes or something that could be improved, please let me know. 
>>>> The tutorial can be found at https://driesvr.github.io/Tutorials/.
>>>>
>>>> Kind regards
>>>>
>>>> Dries
>>>>
>>>>
>>>>
> 在 2017年7月19日星期三 UTC+8下午8:00:59,Dries Van Rompaey写道:
>>
>> Hi,
>>
>> The MM simulations in the tutorial are intended to allow the system to 
>> relax and to find suitable cell dimensions. We do this at the MM level 
>> because it's rather fast when compared to QMMM. The relaxed system is then 
>> moved to the QMMM level in order to simulate bond breaking. 
>>
>> The reaction is not sampled in the *unbiased* QMMM, which is why we add 
>> metadynamics in the second part. Once we bias the collective variable, you 
>> can see the reaction occurring at the QMMM level.
>>
>>
>> Op woensdag 19 juli 2017 13:34:52 UTC+2 schreef jts2... at gmail.com:
>>>
>>> Hi Dries,
>>>
>>> I have read the tutorial and wonder how could I show the advantage of 
>>> QMMM calculation over MM calculation. Should I run a complete MM simulation 
>>> and compare the two results ? I notice that you said in the tutorial that 
>>> the reaction is not achieved in the simulation. Does that mean QMMM method 
>>> doesn't work in this simulation ? 
>>>
>>> 在 2017年7月18日星期二 UTC+8下午2:49:11,Dries Van Rompaey写道:
>>>>
>>>> Hi cp2k-users,
>>>>
>>>> After experimenting with cp2k for a while I have written down a short 
>>>> tutorial on how to use cp2k for biochemical systems. The tutorial covers 
>>>> the setup of an enzyme system with ambertools followed by equilibration 
>>>> with cp2k at the MM level, after which we move the system to QM/MM for 
>>>> metadynamics simulations of an enzymatic reaction. I am far from an expert 
>>>> myself, but I thought this might be useful to people starting out. If you 
>>>> spot any mistakes or something that could be improved, please let me know. 
>>>> The tutorial can be found at https://driesvr.github.io/Tutorials/.
>>>>
>>>> Kind regards
>>>>
>>>> Dries
>>>>
>>>>
>>>>
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