Comparative Molecular Dynamics and Monte Carlo Study of Statistical Properties for Coarse-Grained Heteropolymers

TL;DR

This study compares thermodynamic properties of coarse-grained heteropolymers using molecular dynamics and Monte Carlo methods, revealing qualitative agreement but significant quantitative differences depending on the thermostat used.

Contribution

It provides a systematic comparison of thermodynamic results from different simulation techniques and thermostats for heteropolymer models, highlighting discrepancies and their causes.

Findings

Qualitative agreement between methods

Quantitative differences with Nose-Hoover thermostat

Autocorrelation analysis of simulation data

Abstract

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