Photoactive yellow protein (PYP) is a water-soluble photoreceptor protein consisting of 125 amino acids with a p-coumaric acid anion cofactor. Recent ultrafast studies of fluorescence decay of PYP and several mutants revealed coherent oscillations of about 140 cm-1 and 50 cm-1 attributed to largely chromophore motions and protein matrix vibrations, respectively. Using normal mode analysis with a new force field for PYP in the excited state, we found that modes with frequencies near 130 cm-1 project strongly onto the chromophore and largely correspond to isomerization of the chromophore, strongly enhanced in this direction compared to nearby vibrational modes of the isolated chromophore. We also calculated rates of vibrational cooling of the chromophore and found that this process likely influences the photoisomerization kinetics. We present here an analysis of the vibrations of PYP and several mutants, with emphasis on dynamical coupling between the chromophore and surrounding protein matrix calculated by means of a slightly modified force field from that used in previous work. For the new force field we have adjusted the torsional part by fitting the resulting vibrational modes of the isolated chromophore up to 200 cm-1 to those of ab initio Density Functional Theory (DFT) calculations. We also discuss MD simulations for hydrated PYP and the influence of hydration on energy transfer and dynamical coupling between the chromophore and surrounding protein matrix.