[CP2K:1426] Re: Specifying QM/MM system

[Ghazaleh Zm]

Dear Teo

I am going to do QMMM calculations (DFT/MD/BYLYP) on Thio-AceticAcid in 
CCL4. I don't have parameters for the acid, but I am gonna use Charmm27 for 
the solvent (CCL4). 
Would you please guide me how to prepare the initial structure for the CP2K 
input? using which program? Do I need to have a box and does the acid need 
to be centered in that?

Thanks in advance

Ghazaleh

On Thursday, October 9, 2008 at 11:40:42 PM UTC+2, Teo wrote:
>
> Hi
>
> >  This is not always possible. One of the reasons that you chose QM/ 
> > MM is to eliminate the need for parameters for a certain region of  
> > you system (e.g metalloproteins)
>
> even for metalloproteins you need inevitably to equilibrate the  
> system at MM level. You may want in these cases keep part of the
> region of interest frozen but you've anyway to create potential and  
> topology files for the all system, in order to allow your
> favorite program to run your system.
> Have nice examples regarding metalloproteins where not even 1 ns of  
> MM equilibration are enough to have a proper thermalized
> system.. so thinking to do that at QM level is just too much optimistic.
>
> Let me also stress that as long as you don't want to study chemical  
> reaction classical forcefield can nowadays do an extremely
> good job..
>
> > Just to sweep away all the doubts.. charges for QM atoms, though
> > requested are
> > never used. The only classical contribution coming from QM atoms are
> > the QM-MM non-bonded.
> >
> > I guess that you refer to van der Waals interactions, since the  
> > electrostatic interaction are computed at a QM level.
>
> as I said in the sentence above, MM charges corresponding to QM atoms  
> are ignored. Only classical non-bonded (which could
> also be different  than van der waals) for QM - MM atoms are kept.
> But this are general rules that you can find in whatever basic paper  
> on QMMM.
>
> Teo
>
>
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