Comparative molecular dynamics and Monte Carlo study of statistical properties for coarse-grained heteropolymers

Employing a simple hydrophobic-polar heteropolymer model, we compare thermodynamic quantities obtained from Andersen and Nosé-Hoover molecular dynamics as well as replica-exchange Monte Carlo methods. We find qualitative correspondence in the results, but serious quantitative differences using the Nosé-Hoover chain thermostat. For analyzing the deviations, we study different parameterizations of the Nosé-Hoover chain thermostat. Autocorrelations from molecular dynamics and Metropolis Monte Carlo runs are also investigated.