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

2025/08/21 by Henrik Christiansen, Conradi, Maximilian, Suman Majumder +6
Chemistry · Materials Science · Physics and Astronomy · #Advanced Physical and Chemical Molecular Interactions #FOS: Physical sciences #Material Dynamics and Properties #Quantum, superfluid, helium dynamics #Soft Condensed Matter (cond-mat.soft)

paper · pdf · doi:10.48550/arxiv.2508.15539

openalex publication_date 2025/08/21 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

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 Nosé-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.

Citations

• OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
• The Protein-Folding Problem, 50 Years On
• Canonical dynamics: Equilibrium phase-space distributions
• Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
• Molecular dynamics simulations at constant pressure and/or temperature

Related

• Nonequilibrium Dynamics of the Helix-Coil Transition in Polyalanine
• Coupling Transitions in Helical Polymers: The Case of the Helix-Coil and Coil-Globule Transitions
• Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats
• Thermodynamics of helix-coil transitions studied by multicanonical algorithms
• Phase transitions in homogeneous biopolymers: basic concepts and methods