Monday, January 31, 2011

QM/MM course: who presents what when?

This post opens a thread where people enrolled in the QM/MM course can discuss (or simply let other people know) their preferences for time slots and papers.  Hopefully we can get some kind of agreement before Thursday.  Here is the original mail:

For those of you taking the QM/MM course for credit, you will need to pick an applications paper (from the list) and decide when you want to present it. 

I will cover the first two weeks:  Week 1 will be QM/MM background, and Week 2 will be on the paper by Yang (which I think is the most difficult one).

That means one of you has to be ready to give a presentation in about 3 weeks (February 17).  One option is that we simply choose randomly on Thursday (both weeks and papers).  Another option is that you come to some agreement amongst yourselves before then.  Now you have each others email addresses.

The other dates are: Feb 24, March 10, March 17, March 24,  and March 31

Leave comments below

Positions in Dublin and Oslo

Postdoc position in Trygve Helgaker's group in Oslo (deadline Feb 4!)

Ph.D. position in Computational Infection Biology in Dublin (via Jens Erik Nielsen)

Saturday, January 29, 2011

Skillful writing of an awful research paper

by Royce Murray

Rule 1.
Never explain the objectives of the paper in a single sentence or paragraph and in particular never at the beginning of the paper.

For the rest of the rules click here.

Geometry Optimization of the Active Site of a Large System with the Fragment Molecular Orbital Method

Dmitri G. Fedorov, Yuri Alexeev, and Kazuo Kitaura
J. Phys. Chem. Lett., 2011, 2, pp 282–288

An efficient formulation of the fragment molecular orbital method is introduced based on dividing the system into frozen and polarizable domains. The former is computed once taking into account the many-body polarization of the whole system, while the latter is recalculated for each step of a geometry optimization. We performed ligand docking and calibrated the method on the complexes of the Trp−cage miniprotein construct (PDB: 1L2Y) with neutral and charged ligands and applied it to optimize a partially solvated structure of prostaglandin H(2) synthase-1 in complex with the reversible competitive inhibitor ibuprofen (PDB: 1EQG) containing 19471 atoms at the B3LYP-D/6-31G* and RHF/STO-3G levels of theory for the polarizable and frozen domains, respectively. The optimization took 32 h on six dual CPU quad-core 2.83 GHz Xeon nodes. Our method requires no fitted parameters and allows optimizations of large systems based solely on quantum mechanics.