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. 2012 Feb 8;102(3):649–660. doi: 10.1016/j.bpj.2011.12.021

Figure 5.

Figure 5

(a) Site 1 autocorrelation functions using MD and AR(1) processes generated with time constant equal to 2 fs, 5 fs, and 50 fs at 77 K and 300 K. (b) Site 1 population dynamics of MD and AR(1) processes with the different time constants at 77 K and 300 K. (c) The change of pairwise coherence between site 1 and 2 of MD and AR(1) processes with the different time constants at 77 K and 300 K. (d) Spectral density of site 1 of the FMO complex from the MD simulation at 77 K and 300 K. They clearly show the characteristic vibrational modes of the FMO complex. High-frequency modes are overpopulated due to the ultraviolet catastrophe observed in classical mechanics. The Ohmic spectral density used by Ishizaki and Fleming (10) was presented for comparison. The spectral densities of site 1 from AR(1) processes are also presented.