CP2K tutorial for biochemical systems

[Dries Van Rompaey]

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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