In this work we extend classical molecular dynamics by coupling it with an electron transport model known as the two temperature model. This energy balance between free electrons and phonons was first proposed in 1956 by Kaganov et al. but has recently been utilized as a framework for coupling molecular dynamics to a continuum description of electron transport. Using finite element domain decomposition techniques from our previous work as a basis, we develop a coupling scheme that preserves energy and has local control of temperature and energy flux via a Gaussian isokinetic thermostat. Unlike the previous work on this subject, we employ an efficient, implicit time integrator for the fast electron transport which enables larger stable time steps than the explicit schemes commonly used. A number of example simulations are given that validate the method, including Joule heating of a copper nanowire and laser excitation of a suspended carbon nanotube with its ends embedded in a conducting substrate. Published in 2010 by John Wiley & Sons, Ltd.