[gmx-users] QMMM gromacs/CPMD
g.groenhof at rug.nl
Fri Nov 3 22:08:06 CET 2006
(1) For QM/MM, even simple QM solute in a MM solvent, Lennard Jones
parameters are required to compute the Van der Waals interactions
between the QM and MM subsystems.
Thus one always needs to give the atoms types for the atoms in the QM
A simple topology file will do, containing only the [ atoms ] section,
with the atoms of your QM solute. To avoid problems when the QM
subsystem moves over the boundary during a simulation, it is advisable
to define the bonds between the atoms as well, using bondtype 5 in the
[ bonds ] section. This bondtype does not have a function nor
parameters, but allows gromacs to make the molecule whole again before
every QM computation.
(2) You can try prdrg.
(3) QM/MM Electrostatics inside CPMD are handled different from the
electrostatics in gromacs. The precise details I do not know. Maybe
Pradip Kumar Biswas can add something to this?
(4). Setting the cut-off to 0 means infinite cut-off, and works in
vacuum only. For pbc, use a finite cut-off and PME or ReactionField. I
suppose the example you are talking about concerns a minimization of
some QM/MM system in vacuo.
On Nov 3, 2006, at 4:35 PM, Loison Claire wrote:
> Dear gmx-users,
> I would like to test the gromacs/CPMD combinaison for QMMM
> For the system I am interested in, the configuration is "relatively
> simple", the model contains
> a single quantum solute molecule surrounded by classical solvent
> molecules (water, let say).
> So no broken bonds, and no dummy atoms. But it's complicated because
> it's a liquid phase.
> So i want to build the topology, including for example the
> "solute.itp" file.
> What puzzles me, is that i should give some information about a
> classical force field
> describing the atoms in my quantum solute... But i cannot set in
> advance agood classical force field for it:
> If I had, i would not bother about QMMM.
> So I have several questions about the gromacs/CPMD:
> (1) does gromacs use at the force-field parameters concerning the
> quantum atoms ?
> When and for what ? How critical are those parameters ?
> (2) i think about building a quick and dirty approximate classical
> force field for my solute molecule, in order to
> create classically a starting point before doing the QMMM. But of
> course as my force-field is probably bad,
> the system may explode as soon as i change the model. So do you have
> some advise how to construct my first system ?
> (3) an other question which is more CPMD related : i am now testing
> the influence of size of the quantum bounding box
> and the poisson solver on the electronic structure of my solute.
> As i understood, this SYMMETRY 0 is in order to avoid
> seeing the electrostatic periodic images which
> are instrinsically present in plane-wave calculation.
> In vacuum it's exactly what i want. But my QMMM system is a liquid, i
> want to have periodic
> boundary conditions for my MM box (the gromacs'one, not the CPMD one).
> What does the QM system feel if i take the ususal pbc of gromacs
> input ? Does it see its
> periodic images (I mean with the periodicity of the MM box ) ?
> Do i have to take care that the QM system does not cross the boundary
> of the MM box ?
> (4) in the examples from the Gogonea's group (
> which i had difficulties to run, by the way), the gromacs cutoff for
> the electrostatic interaction is set to 0.
> Is that compulsory ?
> Thanks for any suggestions and for your understanding about confused
> Claire Loison
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