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;
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(1)phe.cmd - SQM input to calculate the QM energy of toluene
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(2)phe.out - SQM output from the QM energy calculation
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(3)phe_qmmm.cmd - SQM input to calculate the QM/MM energy of toluene
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(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