[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
>>>>>>>
>>>>>>>
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