CP2K tutorial for biochemical systems

[jts2t... at gmail.com]

Thanks for your patience !



在 2017年7月19日星期三 UTC+8下午9:40:39，Dries Van Rompaey写道：
>
> 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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