Effective Temperature Characterizing the Folding of a Protein

Details Effective Temperature Characterizing the Folding of a Protein Effective Temperature Characterizing the Folding of a Protein

2006-09-27

arxiv.org/abs/cond-mat/0609680v1

Physics

Condensed Matter

Statistical Mechanics

Scientific paper

The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for inherent structures are introduced and from these quantities an effective temperature is defined. The effective temperature follows the time evolution of a slow relaxation process and reaches the bath temperature when the system is equilibrated. We show that the nonequilibrium system is described by two temperatures, one for fast vibration and the other for slow configurational relaxation, while the equilibrium system is by one temperature. The proposed formalism is applicable widely for the systems with many metastable states.

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