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

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.