Abstract
Molecular dynamics simulations on BPTI in water and in vacuum have been analyzed by Principal Component Analysis and Spectral Analysis. The solvent causes the internal motion of the protein to be more diffusive in character and introduces transitions absent in vacuum. The Spectral Analysis reveals that the presence of water also shifts the spectrum to higher frequencies. This is qualitatively explained by the damping effect of the solvent. By calculating the friction matrix it is found that the first 30 principal components are overdamped.
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