Eur. Phys. J. E (2016) 39: 5
https://doi.org/10.1140/epje/i2016-16005-x

Regular Article

Wang-Landau simulation of Gō model molecules

Institut für Physik, Martin-Luther-Universität, D-06099, Halle (Saale), Germany

^* e-mail: wolfgang.paul@physik.uni-halle.de

Received: 24 November 2015
Accepted: 4 January 2016
Published online: 27 January 2016

Abstract

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.