[CP2K-user] CP2K tutorial for biochemical systems

[Tianshu Jiang]

Hi Qing,

The same situation occurred in my run, but it is remained to be solved.
Have you solved the problem in your simulation afterwards ?



在 2017年12月14日星期四 UTC+8下午9:27:48，Qing Feng写道：
>
> Hi Dries,
>     Thanks for you tutorial on biochemical systems. After seeing this 
> tutorial ,I make some try on RNase systems. In order to save time ,I only 
> chose four bases for simulation. But when I simulated a full QM/MM system, 
>
> I got the following error.
>
>   
> *******************************************************************************
>
>
>   Translating the system in order to center the QM fragment in the QM box.
>  WARNING| Particles:    5387     93 at distance [au]:     0.82969217 less 
> than:      0.95400000; increase EMAX_SPLINE.
>
>
>  *******************************************************************************
>  *   ___                                                                  
>      *
>  *  /   \                                                                  
>     *
>  * [ABORT]                                                                
>      *
>  *  \___/                GEOMETRY wrong or EMAX_SPLINE too small!          
>     *
>  *    |                                                                    
>     *
>  *  O/|                                                                    
>     *
>  * /| |                                                                    
>     *
>  * / \                                              
>  fist_neighbor_lists.F:607 *
>
>  *******************************************************************************
>    I don't know why this problem occur .   Could you help me to see if 
> there are any problems.
>    
>   For helping your understanding, I attach my files. Thank you in advance!
>   
>   Best wishes!
>   
>   Qing
>
>  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/ as 
>> well as on the main cp2k wiki: https://www.cp2k.org/howto:biochem_qmmm. 
>>
>> Kind regards
>>
>> Dries
>>
>>
>>
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