CP2K tutorial for biochemical systems

Dries Van Rompaey dries.va... at gmail.com
Fri Jul 21 17:14:28 CEST 2017


You're welcome.

The tutorial has been updated with a brief section on how to include enzyme 
residues in the QM region. As always, comments and improvements are welcome.

Op donderdag 20 juli 2017 03:15:40 UTC+2 schreef jts2... 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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