title: On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations.
abstract: In a molecular dynamics (MD) simulation, various thermostat algorithms, including Langevin dynamics (LD), Nosé-Hoover (NH), and weak-coupling (WC) thermostats, can be used to keep the simulation temperature constant. A canonical ensemble is generated by the use of LD and NH, while the nature of the ensemble produced by WC has not yet been identified. A few years ago, it was shown that when using a WC thermostat with particular values of the temperature coupling time for liquid water at ambient temperature and pressure, the distribution of the potential energy is less wide than the canonical one. This led to an artifact in temperature replica-exchange molecular dynamics (T-REMD) simulations in which the potential energy distributions appear not to be equal to the ones of standard MD simulations. In this paper, we re-investigate this problem. We show that this artifact is probably due to the ensemble generated by WC being incompatible with the T-REMD replica-exchange criterion, which assumes a canonical configurational ensemble. We also show, however, that this artifact can be reduced or even eliminated by particular choices of the temperature coupling time of WC and the replica-exchange time period of T-REMD, i.e., when the temperature coupling time is chosen very close to the MD time step or when the exchange time period is chosen large enough. An attempt to develop a T-REMD replica-exchange criterion which is likely to be more compatible with the WC configurational ensemble is reported. Furthermore, an exchange criterion which is compatible with a microcanonical ensemble is used in total energy REMD simulations.
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland.
authors.forename: Zhixiong
authors.initials: Z
authors.lastname: Lin
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Switzerland.
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Gunsteren