CP2K tutorial for biochemical systems

[jts2t... 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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