Influence of Thermostats on the Dynamics of the Helix-Coil Transition

TL;DR

This study compares how three different thermostats affect the nonequilibrium dynamics of helix-coil transition in polyalanine using all-atom molecular dynamics simulations, revealing small phenomenological differences but quantitative variations.

Contribution

It provides a systematic comparison of Langevin, Andersen, and Nosé-Hoover thermostats on helix-coil transition dynamics in polyalanine.

Findings

Small phenomenological differences observed among thermostats

Quantitative differences in dynamics for the three thermostats

Insights into thermostat influence on protein folding simulations

Abstract

We present results from all-atom molecular dynamics simulations for the nonequilibrium dynamics of the collapse and helix-coil transition in polyalanine. In particular, we compare the influence of three different thermostats, viz., the Langevin, Andersen, and Nos\'e-Hoover thermostats. For that purpose, we investigate the nonequilibrium pathways of the transition from the high-temperature random-coil state to the low-temperature helical state. Additionally, we analyze the time evolution of the potential energy and temperature. Our results show only small differences in the observed phenomenology, albeit quantitatively the dynamics appear to be different for the three thermostats.