[gmx-developers] QMMM, exclusions and neighbor search
Pia Toelle
pia.toelle at bccms.uni-bremen.de
Mon Mar 8 11:00:38 CET 2010
Hi.
So what's about my idea just to set the QM-QM interaction in
"sys->ffparams" (in topio.c) to zero by including special QM-atomtypes.
Do you see any problem there? For me it seems to work.
Pia
Berk Hess wrote:
> Hi,
>
> With PME you can not easily exclude Coulomb interactions between atom
> pairs that come from
> the PME mesh part. You would need one or multiple (I don't recall now)
> extra mesh calculations
> to do that. It can be done, but requires some coding effort.
>
> Berk
>
> Pia Toelle wrote:
>> Hello.
>>
>>
>> Actually, we are using PME (and our QM-calculation also uses pbc with
>> Ewald summation). What problem do you refer to?
>>
>>
>> Best wishes,
>> Pia
>>
>>
>> Berk Hess wrote:
>>
>>> Hi,
>>>
>>> I suggested a simple solution for this problem to Gerrit, which does not
>>> require code changes,
>>> except for a check in grompp.
>>>
>>> I think you can simply use energy group exclusions by putting all the qm
>>> atoms in a separate
>>> energy group and using: energygrp_excl = qm qm
>>> This should do what you want, except when using PME and to a certain
>>> extent also reaction field.
>>> But for those methods it is quite complicated to come up with a proper
>>> scheme.
>>>
>>> Berk
>>>
>>> Pia Toelle wrote:
>>>
>>>> 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
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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
>>>>>>>>> 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
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>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> gmx-developers mailing list
>>>>>> gmx-developers at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
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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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