[gmx-developers] QMMM, exclusions and neighbor search

Pia Toelle pia.toelle at bccms.uni-bremen.de
Tue Aug 11 13:10:53 CEST 2009 

Okay.

Thanks for your reply. I will try to do so.
Please, tell me if their are any news concerning this problem.

Cheers,
Pia

Berk Hess wrote:
> Hi,
> 
> That would work.
> But we should certainly fix the code.
> I did not think of this situation when introducing the moltype data
> structure in version 4.0.
> 
> Berk
> 
> Pia Toelle wrote:
>> Hello.
>>
>> To avoid a different handling of QM-atoms of different molecule types,
>> would it be possible to put all QM atoms in one molblock and moltype, as
>> the molblocks ans moltypes are filled and defined anyway in
>> generate_qmexcl? Or would this influence other parts of the program?
>>
>> greetings
>> Pia
>>
>>
>> Gerrit Groenhof wrote:
>>   
>>> Hi,
>>>
>>> I had not realized your previous question had not been answered
>>> completely, sorry.
>>>
>>> In 3.3 it was a bit more intuitive, also for me.
>>>
>>> In the generate_qmexcl there is a loop over all molblocks. Thus all qm
>>> atoms are found, even if they are in different molecules. However, you
>>> might have a point that between molecules the qm atoms do not seem to
>>> get excluded. Such situation could happen, for example if part of the
>>> protein and a few waters are treated at the QM level, which is typical
>>> for enzymes. To avoid problems (if any), you can include such waters in
>>> the .itp file of the protein.  But it should work also with the
>>> different QM atom in different topologies and I will  look into this .
>>>
>>> Best,
>>>
>>> Gerrit
>>>
>>>
>>>
>>>
>>>
>>> On 10 Aug 2009, at 18:27, Pia Toelle wrote:
>>>
>>>     
>>>> Hello.
>>>>
>>>> I still have problems with "generate_qmexcl" in version 4.0.5.
>>>>
>>>> Comparing to earlier version 3.3.3, one notices that the data structure
>>>> moltype and molblock are included. In the earlier version, qm exclusions
>>>> were generated for each QM-atom inside the system, now in version 4.0.5,
>>>> they are generated per atom inside each molecule type.
>>>>
>>>> I still wounder whether the exclusions between QM-atoms of different
>>>> molecule types are considered here and - if yes - how. Or - if not -
>>>> where this is done.
>>>>
>>>> Is the splitting of the QM part into molblock's correct?
>>>>
>>>> I would be glad for any comment or reply! Please tell me if my question
>>>> is not precise.
>>>>
>>>> Pia
>>>>
>>>>
>>>>
>>>> Pia Toelle wrote:
>>>>       
>>>>> Hello Gerrit.
>>>>> Thanks for the reply, it helped a lot, but I still have some problems to
>>>>> understand.
>>>>>
>>>>>
>>>>> As far as I understood in "generate_qmexcl" the QM molecules are put
>>>>> into separate molblock and each molecule has its own moleculetype.
>>>>> Then "generate_qmexcl_moltype" is called and the exclusions are set.
>>>>>
>>>>> At first an array "qm_arr" is generated. As the loop
>>>>> "for(i=0;i<molt->atoms.nr;i++)" only passes through the atoms with the
>>>>> same moleculetype.
>>>>> "sys->moltype[--].excls" contains the exclusions between Atoms of the
>>>>> same topologie.
>>>>>
>>>>> Are the nonbonded interactions listed in the ilist and excluded by
>>>>> deleting them in this list?
>>>>>
>>>>> Where is the ilist generated in first place?
>>>>>
>>>>>
>>>>> Please correct my estimates.
>>>>> Cheers,
>>>>>
>>>>> Pia
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Gerrit Groenhof wrote:
>>>>>         
>>>>>> The QM - QM interactions, both Coulomb and van der Waals are explicitly
>>>>>> exluded.
>>>>>>
>>>>>> The code for this begins with the comment
>>>>>>
>>>>>>  /* creating the exclusion block for the QM atoms. Each QM atom has
>>>>>>   * as excluded elements all the other QMatoms (and itself).
>>>>>>   */
>>>>>>
>>>>>> In generate_qmexcl_moltype (topio.c).
>>>>>>
>>>>>> Thus the exclusionlists are expanded with all QM- QM interactions.
>>>>>> The coulomb interactions are handled a bit more dirty: In the
>>>>>> initialisation (qmmm.c), these charges are put to zero.
>>>>>> Thus the standard nbsearching will look at the exclusions and check
>>>>>> if a
>>>>>> particle is charged. This way it will never include the QM QM  atom
>>>>>> pairs, or QM MM coulomb interactions.
>>>>>> The QMMM nbsearching in the next step takes the QM atoms as i-particles
>>>>>> and searches all MM neighbours.
>>>>>>
>>>>>> Best wishes,
>>>>>>
>>>>>> Gerrit
>>>>>>
>>>>>>
>>>>>> On 15 Jul 2009, at 20:10, Pia Toelle wrote:
>>>>>>
>>>>>>           
>>>>>>> Hello
>>>>>>>
>>>>>>> (I am using Gromacs 4.0.5 (QM/MM))
>>>>>>>
>>>>>>> I have a question about the exclusion of nonbonded (specially VdW)
>>>>>>> interaction in QM/MM simulation. The coulomb and VdW interaction
>>>>>>> between
>>>>>>> two QM Atoms should not be calculated by Gromacs as the QM-QM
>>>>>>> interaction is done by the QM-program.
>>>>>>> Where (and how) in the code is the VdW (and also coulomb) interaction
>>>>>>> between two QM atoms excluded?
>>>>>>>
>>>>>>> Please also comment on the following:
>>>>>>>
>>>>>>> (topio.c called by grompp.c)
>>>>>>> "generate_qmexcl" and "generate_qmexcl_moltype", here the
>>>>>>> exclusions for
>>>>>>> the INTRA-molecular interaction are set. Is this right? What is about
>>>>>>> the Interaction between different QM-Molecules?
>>>>>>>
>>>>>>> (ns.c)
>>>>>>> In "search_neighbours" the "nsgrid_core" is called to set up the
>>>>>>> neighbor lists (for all atoms QM and MM !?), then it is called to
>>>>>>> set up
>>>>>>> the QM/MM neighbor list.
>>>>>>>
>>>>>>> (force.c)
>>>>>>> In "do_forces" the "do_force_lowlevel" is called, there the
>>>>>>> QM-calculation and "do_nonbonded" takes place. The later does not
>>>>>>> contain any information about the atom being QM or not, as far as I
>>>>>>> can
>>>>>>> see. Therefore, I believe, that the decision to calculate VdW was made
>>>>>>> by setting up the lists. Is this right???
>>>>>>>
>>>>>>>
>>>>>>> Thanks in advance,
>>>>>>> Pia Tölle
>>>>>>>
>>>>>>> BCCMS, university of Bremen, Germany
>>>>>>> _______________________________________________
>>>>>>> gmx-developers mailing list
>>>>>>> gmx-developers at gromacs.org
>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>>>> www interface or send it to gmx-developers-request at gromacs.org.
>>>>>>>             
>>>>>> -- 
>>>>>> Gerrit Groenhof
>>>>>> MPI biophysical chemistry
>>>>>> Goettingen
>>>>>> Germany
>>>>>> http://wwwuser.gwdg.de/~ggroenh/
>>>>>>
>>>>>> _______________________________________________
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>>>>>>           
>>>>> _______________________________________________
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>>>>>         
>>>> _______________________________________________
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>>>>       
>>> -- 
>>> Gerrit Groenhof
>>> MPI biophysical chemistry
>>> Goettingen
>>> Germany
>>> http://wwwuser.gwdg.de/~ggroenh/
>>>
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>>>     
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