[gmx-developers] QMMM, exclusions and neighbor search

Mon Mar 8 09:13:26 CET 2010

Hi Gerrit.

I made the following changes in  src/kernel/topio.c:

- "generate_qmexcl": "molblock" filling changed (I am not sure, if this
was related to the QM-QM interaction problem)

- added "generate_qm_atom_type": new QM-atomtype for all atomtypes added
 ( sys->atomtypes.nr were doubled)
The added QM-atomtypes have zeros in sys->ffparams for the QM-QM
non-bonded interaction.

I hope, that the changes in the attached file topio.c are understandable
and that it will help you.

Greetings,
Pia

Gerrit Groenhof wrote:
> Hallo Pia,
> 
> Sorry for not getting back on this issue earlier. 
> 
> Have you been able to fix this bug?
> 
> BEst wishes,
> 
> Gerrit
> 
> 
> On 11 Aug 2009, at 13:10, Pia Toelle wrote:
> 
>> 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/
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> gmx-developers mailing list
>>>>>>>> gmx-developers at gromacs.org
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>>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
>>>>>> _______________________________________________
>>>>>> gmx-developers mailing list
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>>>>>>
>>>>> -- 
>>>>> Gerrit Groenhof
>>>>> MPI biophysical chemistry
>>>>> Goettingen
>>>>> Germany
>>>>> http://wwwuser.gwdg.de/~ggroenh/
>>>>>
>>>>> _______________________________________________
>>>>> gmx-developers mailing list
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>>>>>
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>>>>
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>> _______________________________________________
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> 
> --
> Gerrit Groenhof
> MPI biophysical chemistry
> Goettingen
> Germany
> http://wwwuser.gwdg.de/~ggroenh/
> 

-- 

Pia Tölle
BCCMS, Universität Bremen

Building TAB, Room 3.15
Am Fallturm 1A
D-28359 Bremen

Phone: +49 (0)421 218 7762
Fax: +49 (0)421 218 4764
Email: toelle[at]bccms.uni-bremen.de
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