[gmx-users] QMMM gromacs/CPMD
cloison at lasim.univ-lyon1.fr
Fri Nov 3 16:35:35 CET 2006
I would like to test the gromacs/CPMD combinaison for QMMM calculations.
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"
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
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