• NVE: The microcanonical ensemble, where the system is kept from changes in moles (N), volume (V), and energy (E). This set-up is an example of an adiabatic process.

  • NVT: The canonical ensemble, where the system is kept from changes in moles (N), volume (V), and temperature (T). This set-up is also known as constant-temperature molecular dynamics, and requires a thermostat.

  • NPT: The isothermal-isobaric ensemble, where the system is kept from changes in moles (N), pressure (P), and temperature (T). Both a thermostat and barostat are needed.

  • NPH: The system is kept from changes in moles (N), pressure (P), and enthalpy (H). Enthalpy is held constant when the pressure is fixed without temperature control.

  • NST: The system is kept under constant-temperature and constant-stress conditions. It is closely related to the NPT ensemble. Hydrostatic pressure is applied uniformly (isotropically), and the components of the stress tensor are controlled. It is good for studying the stress-strain relationship of polymers or metals.

Regulators

  • Langevin Dynamics (NVT or NPT): attempts to mimic solvent viscosity by introducing things that occasionally cause friction and perturb the system. When used to control temperature, a small damping constant, γ, should be used.

  • Berendsen Thermostat: the system is weakly coupled to a heat bath at a set temperature. The thermostat doesn’t mirror the canonical ensemble for small systems, but large systems are roughly ok. It uses a leap-frog algorithm to rescale velocities of particles, controlling temperature.

  • Andersen Thermostat: reassigns a chosen atom or molecule’s velocity given by the Maxwell-Boltzmann statistics for the given temperature.

Solvent Models

  • Implicit Solvent: The solvent is implied and math occurs to make it seem like there’s a solvent. Essentially, the system is held under a polarizable medium defined by the dielectric constant. Think of this like a magician waving a wand–there’s obviously some magic happening, but you can’t actually see it.

  • Explicit Solvent: The solvent is explicitly set in the system and given physical coordinates. Instead of being an audience member seeing the magic show, you’re the magician’s apprentice, and you’re seeing all the little things that go into tricking the audience (like how there’s 2 people in the box being “sawed in half”). TIP3P water is an example of an explicit solvent model.

  • Hybrid Models: These are somewhere between implicit and explicit, and typically found in QM/MM simulations.

  • Gas Phase: This isn’t actually a solvent model, but the lack of a solvent model. All calculations are done in a vacuum.