Lecture: QM/MM

 

Welcome to the QM/MM lecture. If you want to follow on with what I am saying during the lecture, please download this PDF file. It contains a copy of the slides together with the full text of what I am going to say. You can use this to keep up with the lecture, or to review the material at a later point.


During the lecture I will discuss four files. These are;


  1. (1)phe.cmd - SQM input to calculate the QM energy of toluene

  2. (2)phe.out - SQM output from the QM energy calculation

  3. (3)phe_qmmm.cmd - SQM input to calculate the QM/MM energy of toluene

  4. (4)phe_qmmm.out - SQM output from the QM/MM calculation


If you want, please feel free to download and take a look at the above files. They will make a lot more sense during the lecture...


A good reference to gain further understanding of QM/MM for reaction modelling is;


A practical guide to modelling enzyme-catalysed reactions

Lonsdale R, Harvey JN, Mulholland AJ

Chem. Soc. Rev. (2012), vol. 41, pp. 3025-3038

http://dx.doi.org/10.1039/C2CS15297E


A good reference to gain further understanding of QM/MM free energy calculations is;


An efficient method for the calculation of quantum mechanics/molecular mechanics free energies.

Woods CJ, Manby FR, Mulholland AJ.

J. Chem. Phys. (2008) vol. 128 (1) pp. 014109

http://dx.doi.org/10.1063/1.2805379