[gmx-developers] QMMM, exclusions and neighbor search
pia.toelle at bccms.uni-bremen.de
Thu Jul 16 14:38:16 CEST 2009
Thanks for the reply, it helped a lot, but I still have some problems to
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
"sys->moltype[--].excls" contains the exclusions between Atoms of the
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.
Gerrit Groenhof wrote:
> The QM - QM interactions, both Coulomb and van der Waals are explicitly
> 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,
> On 15 Jul 2009, at 20:10, Pia Toelle wrote:
>> (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?
>> 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.
>> 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
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>> gmx-developers at gromacs.org
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> Gerrit Groenhof
> MPI biophysical chemistry
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