One of the strengths of 2D IR spectroscopy is the ability to quantitatively link experimental results to computer simulations, be it molecular dynamics simulations, quantum chemistry calculations, or ideally a combination of both on the level of mixed quantum mechanics/molecular mechanics (QM/MM) calculations. In the present chapter, we outline how such simulations are performed and present some examples with computer code that can be reproduced on a personal computer. We also describe more sophisticated models that have been developed. The motivation of the chapter is not to get the most accurate agreement with experiment, but to outline the essential concepts with working examples. In this chapter we use the molecular dynamics simulation package Gromacs 3.3 [183] (which can be downloaded for free from http://www.gromacs. org), the quantum chemistry program Gaussian09 for electronic structure calculations [58], and simple Mathematica or C codes (together with Numerical Recipes routines [152]). All the relevant computer programs in this chapter can be downloaded from the book webpage (http://www.2d-ir-spectroscopy.com), so the reader has operational programs to start with which can then be modified at will. For each of the Mathematica programs, Matlab versions are available on the book webpage as well. 2D lineshapes: Spectral diffusion of water Perhaps the most accurate quantities that can currently be modeled are 2D IR lineshapes.
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