Hi Claire,
[EMAIL PROTECTED] wrote: -----To: gmx-users@gromacs.org
From: Loison Claire <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
Date: 11/03/2006 10:35AM
Subject: [gmx-users] QMMM gromacs/CPMD
Dear gmx-users,
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"
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.
pb> right. All you need to provide is the topology and any guess/garbage
parameter for the electrostatic and all bonded interactions. But you need
some consistent parameter for the Lennard-Jones since QM/MM Hamiltonian does
not couple the LJ interaction and they are evaluated in Gromacs.
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 ?
pb> Only LJ interaction parameters between QM and MM atoms are important but
none of the others (ESP charge, and any bonded 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 ?
pb> provide any value for the ESP charges and some 'good' guess for the LJ.
provide any values for the bond, angle dihedral, etc; they won't matter.
(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 ) ?
pb> No, QM won't see any periodic image of MM. it works with a Coulomb cut-off.
**I saw an uncorrected typo in the official version of CPMD-3.11.1 which is related
to the consideration of QM/MM interaction from second and third layers (note: the MM atoms
are divided into 3 different layers for the QM so that simple approximations be made for
the distant water molecules. The typo won't affect you if you choose a QM/MM Coulomb cutoff
large enough so that the code includes all your MM atoms in the first MM layer
(look at your CPMD_inp.run).
Do i have to take care that the QM system does not cross the boundary of
the MM box ?
pb> No. For QM, the interface translates the atoms to the center of the QM box
and this translation is invissible to MM.
(4) in the examples from the Gogonea's group (
http://comppsi.csuohio.edu/groups/qmmm.html,
which i had difficulties to run, by the way),
pb> what sort of?
the gromacs cutoff for
the electrostatic interaction is set to 0.
pb> where? Anyway, the Gromacs electrostatic cutoff and QM/MM electroststic
cutoff are independent. So that, you can have PME for MM but your convenient
cutoff for QM; choice and consequences are yours.
Is that compulsory ?
pb> No.
cheers,
pb.
Thanks for any suggestions and for your understanding about confused
questions..
Claire Loison
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