[gmx-users] QMMM gromacs/CPMD

Loison Claire cloison at lasim.univ-lyon1.fr
Fri Nov 3 16:35:35 CET 2006

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" 
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

More information about the gromacs.org_gmx-users mailing list