Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms

TL;DR

This paper develops and tests momentum rescaling formulas for various constant-temperature algorithms in replica-exchange molecular dynamics, ensuring correct canonical ensemble sampling.

Contribution

It introduces new momentum rescaling methods for Langevin, Andersen, Nosé-Hoover, and Nosé-Poincaré thermostats in replica-exchange MD, extending previous work limited to Gaussian constraints.

Findings

Proper rescaling is essential for accurate canonical ensemble sampling.

The proposed formulas are effective in small biomolecular systems.

Correct rescaling improves the reliability of replica-exchange simulations.

Abstract

In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had previously been worked out only for the Gaussian constraint method. In this letter, we present momentum rescaling formulae for four other commonly used constant-temperature algorithms, namely, Langevin dynamics, Andersen algorithm, Nos\'{e}-Hoover thermostat, and Nos\'{e}-Poincar\'{e} thermostat. The effectiveness of these rescaling methods is tested with a small biomolecular system, and it is shown that proper momentum rescaling is necessary to obtain correct results in the canonical ensemble.