[CP2K-user] GEOMETRY wrong or EMAX_SPLINE too small

刘小凤 10751... at qq.com
Fri Apr 16 14:25:51 UTC 2021


hello everyone
I have the same question GEOMETRY wrong or EMAX_SPLINE too small!  Has 
anyone know function of EMAX_SPLINE ?  In this example 
https://www.cp2k.org/exercises:2016_uzh_cmest:first_simulation_run?s[]=spline ,Why 
set EMAX_SPLINE 10000?
EMAX_SPLINE 10000
  
在2021年1月27日星期三 UTC+8 上午2:14:59<fa... at gmail.com> 写道:

> Dear Aashish,
>
> The potential energy reported in the last MD step indicates that your 
> system is blowing up: POTENTIAL ENERGY[hartree]    =          
> 0.591818899590E+03  -0.982542787069E+03 
> A positive potential energy is always a bad sign. Your initial 
> configuration must be unstable. How did you perform the previous NVT and 
> NPT?
>
> Cheers,
> Fabian
> On Tuesday, 26 January 2021 at 18:42:06 UTC+1 mert... at gmail.com wrote:
>
>> 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
>>>>>>>
>>>>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20210416/feb264fa/attachment.htm>


More information about the CP2K-user mailing list