CP2K tutorial for biochemical systems

[Qing Feng]

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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