[CP2K-user] GEOMETRY wrong or EMAX_SPLINE too small

[Mert Sağıroğlugil]

I dont know why all the quantities calculated had been written as NaN, they 
must have some values. Seems like the biggest problem of all about your md 
simulation. Just followed the same tutorial and worked pretty fine with the 
same files they have provided.  Have you used the same files on the 
tutorial ? 


On Monday, January 25, 2021 at 3:31:17 PM UTC+3 Aashish Bhatt wrote:

> Dear sir
>
> I have run the complete system in the cp2k. previously it was in NAMD.
> I have perform Minimisation, NVT, NPT and then NVT(QM/MM) dynamics . In 
> the dynamics i am getting the following error message.
> I am also attaching the input file.
>
> Please help me to overcome this issue.  
>
>
>  *******************************************************************************
>  ENSEMBLE TYPE                
> =                                              NVT
>  STEP NUMBER                  
> =                                               59
>  TIME [fs]                    =                                        
> 29.500000
>  CONSERVED QUANTITY [hartree] 
> =                                              NaN
>
>                                               INSTANTANEOUS             
> AVERAGES
>  CPU TIME [s]                 =                       43.02                
> 27.26
>  ENERGY DRIFT PER ATOM [K]    =                         
> NaN                  NaN
>  POTENTIAL ENERGY[hartree]    =          0.591818899590E+03  
> -0.982542787069E+03
>  TOTAL KINETIC ENERGY[hartree]=                         
> NaN                  NaN
>  QM KINETIC ENERGY[hartree]   =                         
> NaN                  NaN
>  TOTAL TEMPERATURE[K]         =                         
> NaN                  NaN
>  QM TEMPERATURE[K]            =                         
> NaN                  NaN
>  PRESSURE [bar]               =                         
> NaN                  NaN
>
>  *******************************************************************************
>
>
>   Translating the system in order to center the QM fragment in the QM box.
> ip, j, pos, lat_pos      1     1         NaN         NaN         
> NaN         NaN
>
>
>  *******************************************************************************
>  *   
> ___                                                                       *
>  *  /   
> \                                                                      *
>  * 
> [ABORT]                                                                     
> *
>  *  \___/   QM/MM QM atoms must be fully contained in the same image of 
> the QM *
>  *    |                box - No wrapping of coordinates is 
> allowed!            *
>  *  
> O/|                                                                        *
>  * /| 
> |                                                                        *
>  * / \                                                        
> qmmm_force.F:141 *
>
>  *******************************************************************************
>
>
> On Friday, January 22, 2021 at 11:27:21 PM UTC+5:45 mert... at gmail.com 
> wrote:
>
>> Looks pretty straight forward standard input file.
>> Please check the temperatures first. Did you give enough time to 
>> equilibrate before the QMMM MD run ? 
>>
>> On Friday, January 22, 2021 at 6:10:51 PM UTC+3 Aashish Bhatt wrote:
>>
>>> Please find the attached input file.
>>>
>>> Best Regards
>>>
>>> Aashish
>>>
>>> On Friday, January 22, 2021 at 8:07:32 PM UTC+5:30 mert... at gmail.com 
>>> wrote:
>>>
>>>> You might need to check the last few steps of your simulation's output 
>>>> file and look at the QM Temperatures and overall Temperatures. 
>>>> If you provide your input file that would also be helpful.
>>>>
>>>> On Friday, January 22, 2021 at 4:57:34 PM UTC+3 Aashish Bhatt wrote:
>>>>
>>>>> Dear Sir/Ma'am
>>>>>
>>>>> I am trying to run QM/MM simulation but I am getting the following 
>>>>> error.
>>>>>
>>>>>  Translating the system in order to center the QM fragment in the QM 
>>>>> box.
>>>>>  WARNING| Particles:    1800   1773 at distance [au]:     3.06397331 
>>>>> less than:      3.06774235; increase EMAX_SPLINE.
>>>>>  WARNING| Particles:    1800   1774 at distance [au]:     2.74324487 
>>>>> less than:      2.99334167; increase EMAX_SPLINE.
>>>>>
>>>>>
>>>>>  *******************************************************************************
>>>>>  *   ___                                                              
>>>>>          *
>>>>>  *  /   \                                                              
>>>>>         *
>>>>>  * [ABORT]                                                            
>>>>>          *
>>>>>  *  \___/                GEOMETRY wrong or EMAX_SPLINE too small!      
>>>>>         *
>>>>>  *    |                                                                
>>>>>         *
>>>>>  *  O/|                                                                
>>>>>         *
>>>>>  * /| |                                                                
>>>>>         *
>>>>>  * / \                                              
>>>>>  fist_neighbor_lists.F:607 *
>>>>>
>>>>>  *******************************************************************************
>>>>>
>>>>>
>>>>>  ===== Routine Calling Stack =====
>>>>>
>>>>>             7 build_neighbor_lists
>>>>>             6 build_fist_neighbor_lists
>>>>>             5 list_control
>>>>>             4 fist_calc_energy_force
>>>>>             3 velocity_verlet
>>>>>             2 qs_mol_dyn_low
>>>>>             1 CP2K
>>>>>
>>>>> although I have checked the previous mail regarding this error. I am 
>>>>> using the amber force field parameters. I already change the LJ parameter 
>>>>> for the water (H1 and H2) molecule and Ser, Thr, Tyr alcoholic(OH) hydrogen 
>>>>> atom but I am getting the same error again.
>>>>> I am following the link.
>>>>> https://www.cp2k.org/howto:biochem_qmmm
>>>>>
>>>>> Kindly help me or I miss something
>>>>>
>>>>>
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