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We present a new parallelised controller for steering an arbitrary geometric region of a molecular dynamics (MD) simulation towards a desired thermodynamic and hydrodynamic state. We show that the controllers may be applied anywhere in the domain to set accurately an initial MD state, or solely at boundary regions to prescribe non-periodic boundary conditions (PBCs) in MD simulations. The mean molecular structure and velocity autocorrelation function remain unchanged (when sampled a few molecular diameters away from the constrained region) when compared with those distributions measured using PBCs. To demonstrate the capability of our new controllers, we apply them as non-PBCs in parallel to a complex MD mixing nano-channel and in a hybrid MD continuum simulation with a complex coupling region. The controller methodology is easily extendable to polyatomic MD fluids.
- molecular dynamics
- hybrid MD continuum simulations
- boundary conditions
- thermodynamic state