Friday, February 4, 2011

QM/MM course: notes from week 1


Many questions and discussions during the first lecture.  The course is off to a great start. 

We started by drawing dates and papers and a list of who does what can now be found on the course web page.  You are free to switch dates and papers if you can find someone to switch with.

I also briefly introduced the requirements for the extra credit assignment.  There are now more details here.

Points of discussion not covered by the slides

Size of QM region and QM/MM interactions
The most practical way to gauge the whether the division into QM and MM regions is correct is to enlarge the QM region and see if the results change significantly.  This is rarely done.  If I find some references I will put them here.

Covalent QM/MM boundary
Enlarging the QM/MM region will introduce more cuts across covalent bonds, which could increase the error.  However, the cuts will be further away from the active site, so the effect on relative energies should be smaller, and they should converge as the QM region is increased.

I am not aware of any QM/MM study that does not place the cut between the alpha and beta carbon on the side chain (I would very much like to hear about exceptions).  This is due to the fact that QM/MM boundaries are heavily parameterized, and need to be redone for other types of cuts.  This places restrictions on how much the QM region can be enlarged. 

Slide 12: In the link atom method, there are interactions between the MM charges and the link H atom.  It is not really feasible to remove the “H-part” of the density.

QM/MM packages
Slide 16: Most QM/MM methods consist of a QM and MM program hooked together, sometimes by a third piece of software.  The only “fully integrated” package I know of is Qsite, a commercial program from Schrodinger.  Kasper has put up some more info here.
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