Wang-Landau simulation of Gō model molecules
Institut für Physik, Martin-Luther-Universität, D-06099, Halle (Saale), Germany
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Accepted: 4 January 2016
Published online: 27 January 2016
Gō-like models are one of the oldest protein modeling concepts in computational physics and have proven their value over and over for forty years. The essence of a Gō model is to define a native contact matrix for a well-defined low-energy polymer configuration, e.g., the native state in the case of proteins or peptides. Many different potential shapes and many different cut-off distances in the definition of this native contact matrix have been proposed and applied. We investigate here the physical consequences of the choice for this cut-off distance in the Gō models derived for a square-well tangent sphere homopolymer chain. For this purpose we are performing flat-histogram Monte Carlo simulations of Wang-Landau type, obtaining the thermodynamic and structural properties of such models over the complete temperature range. Differences and similarities with Gō models for proteins and peptides are discussed.
Key words: Soft Matter: Polymers and Polyelectrolytes
© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg, 2016