Fully periodic QM/MM simulations

[Jadzia]

Hi everyone, 

@Matt: Thank you very much for the clarification, it was helpful.

Since full QM/MM periodicity is not possible, I now would like to get the 
QM/MM simulation of water working without QM/MM periodicity, but with 
electrostatic embedding (E_COUPL = COULOMB). The QM method is still DFTB3. 
And I have tried almost everything to get it working, but my water 
molecules still fall apart. 
I have tried...

   - different GMAX values in the EWALD section
   - different ALPHA values in the EWALD section
   - different O_SPLINE values in the EWALD section
   - the QM part completely without electrostatics (no POISSON section)
   - DFTB3 with and without dispersion correction
   - different time step sizes
   - Standard BOMD and second generation CPMD
   - ...

Nothing seems to really solve the problem. I have also tried more things 
such as mechanical embedding with and without QM/MM periodicity. 

Here is a link to a sample input package which can be started directly, all 
files included:

https://drive.google.com/open?id=0B-Ij17NhUNZoeUpETFJhS1hpbFE

Any help I would greatly appreciate. 

Many thanks,
Jadzia



On Thursday, September 7, 2017 at 12:26:24 PM UTC+2, Matt W wrote:
>
> Hi again,
>
> sorry I don't really have time to give long enough replies to be clear, so 
> perhaps a bit confusing.
>
> QM-QM coupling is not needed in your case - your QM box is the same size 
> as the QMMM box. It calculates multipole moments of the QM charge 
> distribution and subtracts artificial interactions if the QM box is smaller 
> than QMMM and adds back in correct ones.
>
> QM-MM long range interactions as you say are the about including the ewald 
> summed potential from the classical part - I think that this is not 
> possible except using E_COUPL = GAUSS, which in turn requires DFT. See the 
> paper from Laio et al for details.
>
> There are several different QMMM methods available, and they have 
> different ranges of applicability.
>
> Matt
>
> On Thursday, September 7, 2017 at 10:28:58 AM UTC+1, Jadzia wrote:
>>
>> Thank you for your answer Matt. 
>>
>> Since error messages can be very helpful if they are precise, I would 
>> like summarize my understanding so far related to the error message I have 
>> gotten:
>>
>> QM-QM long range correction not possible with COULOMB coupling.
>>
>>
>> Firstly, from what you wrote I implicitly conclude that the periodic 
>> section which I have added to my input file went into the direction of what 
>> you had in mind when you wrote about including the coupling of the QM 
>> region with the periodic MM images. In this case the above error message 
>> which I got seems to be not fully suitable since I had disabled the QM-QM 
>> long range correction (i.e. the MULTIPOLE section). To my understanding 
>> (which is admittedly incomplete) the problem might be of a more general 
>> nature and summarized as follows: *QM/MM long range correction not 
>> possible with COULOMB coupling*
>> because it seems to cover both cases QM-MM and optionally also QM-QM long 
>> term corrections (if the multipole section is not switched off) for the QM 
>> region. 
>>
>> Secondly, the error message seems to be too general in another aspect, 
>> because you wrote that QM/MM periodic couplings are possible with DFT (and 
>> Coulomb coupling I guess), in which case the error message does not hold in 
>> its current general form. 
>>
>>
>>
>>
>>
>>
>> On Thursday, September 7, 2017 at 9:26:55 AM UTC+2, Matt W wrote:
>>>
>>> As I said, I wasn't sure if there was a periodic correction implemented 
>>> using Coulomb coupling for DFTB/semi-empirical.
>>>
>>> Looks like you just have to run without periodic coupling, or switch to 
>>> DFT to use periodic coupling.
>>>
>>> On Thursday, September 7, 2017 at 4:41:31 AM UTC+1, Jadzia wrote:
>>>>
>>>> Another thing I wonder about: Matt you said that I should keep the 
>>>> section QMMM periodic section so that the QM region feels the potential of 
>>>> the periodically replicated MM region. Which I would call a "MM-QM long 
>>>> range correction". But the error message of my last post states that 
>>>> a QM-QM long range correction is not possible with Coulomb coupling when I 
>>>> add this section. Therefore I wonder if the periodic section which I set up 
>>>> for the MM-QM long range correction was indeed what you had in mind...
>>>>
>>>
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