Molecular dynamics is both a useful and powerful tool that assists in understanding the macro-behavior of systems by following the atomic motion of the chemical system.  The most time-consuming calculation for each time step is the evaluation of the total potential and atomic forces.  The most accurate and time-consuming way of calculating these quantities is through quantum mechanical (QM) methods, but often lower-level molecular mechanical (MM) methods are used to reduce the computational costs of the simulations.  Another method of reducing the computational expense of QM methods is through the use of interpolations (INT) of the QM surface.  Oftentimes, chemical systems of interest, such as the complicated systems of combustion reactions, involve the need to vary the temperature of the system. One way to vary the temperature of the simulation is through the use of a Berendsen thermostat. The Berendsen thermostat makes use of Newton's Law of Cooling and velocity scaling. A thermostat of this type was adapted and written for the Accelerated Molecular Dynamics with Chemistry (AMolDC) code, which is an adaptive, multilevel QM/MM/INT method designed for performing simulation of complex reactive chemical systems.  Successful performance of AMolDC on single molecules with the thermostat shows promise for the future application of the thermostat on large systems of molecules and ultimately on reactive systems.

Adding a Berendsen thermostat to an accelerating molecular dynamics code

247th National Meeting (2014)

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