[CP2K-user] [CP2K:18164] Re: CP2K tutorial for biochemical systems

[Bowen]

I get the same problem after changing ZERO LJ parameters to "0.3019 0.047" 
for water molecules, TYR and SER. 

changeLJSingleType :TYR at HH 0.3019 0.047
changeLJSingleType :SER at HG 0.3019 0.047
changeLJSingleType :WAT at H1 0.3019 0.047
changeLJSingleType :WAT at H2 0.3019 0.047
change charge :41 at N  -0.41427
change charge :41 at H  0.27333
change charge :41 at CA  0.02273
change charge :41 at HA  0.11383
change charge :41 at C  0.59873
change charge :41 at O  -0.56647
change charge :145 at N  -0.41427
change charge :145 at H  0.27333
change charge :145 at CA  -0.05667
change charge :145 at HA  0.13743
change charge :145 at C  0.59873
change charge :145 at O  -0.56647
On Wednesday, 8 June 2022 at 17:32:23 UTC+8 wave... at gmail.com wrote:

> Hi
>
> I love Dries' comic-like molecules. Does anyone know what he used to do 
> this?
>
> Thanks
> Sam
>
> On Wednesday, May 11, 2022 at 12:18:16 PM UTC+2 qingh... at gmail.com wrote:
>
>> Hello Dries, 
>>
>> Thanks for your tutorial! Could you please comment on changing ZERO LJ 
>> parameters to "0.3019 0.047"?
>> Have you done some tests on it? What's the effects of the modification on 
>> water itself? Thanks a lot!
>>
>> All the best,
>> Qinghua
>>
>> On Tuesday, July 18, 2017 at 8:49:11 AM UTC+2 Dries Van Rompaey wrote:
>>
>>> 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/ as 
>>> well as on the main cp2k wiki: https://www.cp2k.org/howto:biochem_qmmm. 
>>>
>>> Kind regards
>>>
>>> Dries
>>>
>>>
>>>

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