Thermostats for molecular fluids undergoing shear flow: Application to liquid chlorine

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Abstract
In this article we show that atomic thermostats which have been used in the past for nonequilibrium molecular dynamics (NEMD) simulations of molecular fluids were incorrectly formulated. The error stems from an incorrect assumption made about the form of the streaming angular velocity. This assumption is incorrect even in the linear regime. One spurious effect of this atomic thermostat is the generation of a nonsymmetric pressure tensor. We outline a general method, based on a variational principle, for calculating the position and orientation dependent streaming velocity. Using this streaming velocity we develop an atomic thermostat for molecular fluids which does not bias the positional or orientational distribution functions for the fluid. The new atomic thermostat is validated in NEMD simulations of liquid chlorine undergoing planar Couette flow.