Calculation of Local Mode Frequencies (Partial Vibrational Density of States) from Classical or AB Initio Molecular Dynamics Simulations
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Development of analytic derivatives techniques in computational quantum chemistry has paved the way towards practically routine algorithms for computation of vibrational spectroscopic properties of even large molecular systems. In popular quantum chemistry codes, algorithms have been encoded that allow practically “black-box” sequential optimization of molecular geometries (in the sense of locating stationary points on potential energy hypersurfaces in Born-Oppenheimer sense) and harmonic vibrational analyses, performed by diagonalization of mass-weighted Hessian matrices. Aside from harmonic vibrational spectra, harmonic vibrational analyses enable a check of the character of the located stationary point on the molecular PES (minimum vs. saddle point of some order). However, the calculations of the previously mentioned type effectively treat isolated molecular species in vacuum, at T = 0 K. Much more often, in realistic applications, one is interested in molecular species embedded in some medium (solvent, solid matrix etc.) at finite temperature, usually much above absolute zero. To account for the variety of different thermally-induced configurations of a molecular system embedded e.g. in a liquid solvent, statistical physics simulations need to be performed (such as, e.g. Monte Carlo – MC or molecular dynamics – MD). In this scientific workflow, we will focus on a method for efficient processing of the results from MD simulations.
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