[gmx-developers] QMMM, exclusions and neighbor search

[Pia Toelle]

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
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use thewww
>> interface or send it to gmx-developers-request at gromacs.org.
> 
> _______________________________________________
> 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.