You might ask why I chose to start with a technical paper which discusses ensembles, thermostats, distributions and which is, frankly, a little nerdy. Why not start with something more spectacular, say from Science or Nature ? Ensembles, thermostats, timesteps and related technical details matter: they are key to performing reliable, predictive atomistic simulations, and making cotact with experiment. The paper I will discuss is closely concerned with these things, and so I start with a brief introduction which discusses basic concepts (including different thermostat approaches). Those thoroughly familiar with these matters can skip this introductory material.
Use of the correct ensemble and thermostat allows comparison with experiment, which should be the bedrock of numerical simulations. Understanding how the algorithm you have chosen works, what its limitations are, and what experiments it can be compared to is a foundation of doing good computational science. An experimental scientist must understand the limitations of their equipment, sources of error and what can actually be measured. A computational scientist must understand the assumptions behind their modelling. It is very common to have a form of folklore about algorithms: the received wisdom within some parts of the molecular dynamics community is that the Berendsen thermostat is good for equilibration while Nose-Hoover is better for production. This is reasonable, but it is rarely justified, and the reasons for the wisdom are often hard to unpick.
We need to be clear about terminology. When performing molecular dynamics simulations we are generally sampling a phase space which is defined by the positions and velocities (or momenta) of the particles. Our algorithm should, in the long time limit, sample all points in the space with equal probability (this is known as ergodicity). The distribution of states of the system we generate form an ensemble (defined by what macroscopic variables we hold fixed: the canonical ensemble fixes particle number, N, volume, V, and temperature T, while the microcanonical fixes energy, E, instead of T). We must use an integrator and choose an integration time step when we propagate the equations of motion. When working in anything other than the micro-canonical ensemble, we need an algorithm to maintain temperature (and possibly pressure), which normally involves at least one parameter that fixes the response time of the system. Before we can start to sample any data, we must equilibrate the system (ensure that all particles in the system are in equilibrium, with no memory of the starting conditions).
Temperature is maintained with a thermostat, which either puts the system in thermal contact with a reservoir, or introduces stochastic (or random) forces drawn from an appropriate distribution. Thermal contact requires a response time, but provides a quantity which should be conserved and can be monitored to ensure accuracy. Stochastic forces do not have a conserved quantity, and do not allow calculation of dynamical quantities, but form the basis of a number of common approached including Langevin dynamics.
The most commonly implemented thermostats are Nose-Hoover, Andersen and Berendsen (all discussed in the book). Andersen involves stochastic forces, Berendsen a velocity rescaling approach (which does not lead to any ensemble) and Nose-Hoover thermal coupling. Berendsen generally leads to fast equilibration as the rescaling of velocities distributes energy through the system, but also has no conserved quantity which can be monitored. The Nose-Hoover thermostat is probably most commonly used, having a conserved quantity and being associated with the canonical ensemble. However, it is non-ergodic in certain limits (notably for the harmonic oscillator), which requires implementation of the more complex Nose-Hoover chains (a chain of thermostats).
Bussi, Donadio and Parrinello (BDP from now on) propose a new algorithm to sample the canonical distribution, using a form of velocity rescaling. In its simplest form, velocity rescaling involves multiplying the velocities of all particles in the system by the same factor when the temperature moves too far from a target temperature. This is a very simple approach, but leads to discontinuities in the velocities, and does not obey any ensemble. BDP propose that, rather than rescaling to a fixed target kinetic energy, they will use a kinetic energy drawn from a canonical distribution, allowing the system to evolve normally between rescaling steps. Neither of these procedures will disturb the canonical distribution, so that the overall algorithm should sample from the canonical distribution. In practice, they alternate steps which evolve the particles and steps which update the kinetic energy, rescaling the velocities after the kinetic energy step. Stochastic dynamics are used to evolve the kinetic energy.
The kinetic energy is updated with a first-order differential equation, which involves a parameter to set the time scale of the response of the thermostat. This equation has clear, well-defined limits: it reduces to the Berendsen thermostat if the stochastic term is set to zero, to pure stochastic velocity rescaling in the limit of zero time scale, and Hamiltonian dynamics (microcanonical ensemble) in the limit of infinite time scale. The algorithm should give rapid equilibration and correct canonical sampling at equilibrium. The authors also demonstrate how the formalism parallels the Nose-Hoover scheme.
Most interestingly, BDP introduce a conserved quantity, which allows the fidelity of the simulation to be monitored. They point out that, during a simulation, we are generating a sequence of points through phase space, and they associate with each point a weight which measures the probability that the point is drawn from the correct, target ensemble. They show that an effective energy can be written in terms of the weight at each point, and derive an analytic formula for this energy, in terms of an integral along the overall trajectory. The conservation of this effective energy can be used to monitor the effect of integration timesteps on the simulation.
The algorithm is tested for two systems: a Lennard-Jones potential for argon, and water using the TIP4P potential. They check the sampling of the canonical ensemble by monitoring fluctuations, and compare to the Nose-Hoover thermostat for both solid and liquid Lennard-Jones systems. The two approaches compare well for various values of the time scale, though the non-ergodicity of the Nose-Hoover thermostat appears for large values of this parameter. For this simple system, they find that relatively large timesteps (up to 5fs) lead to stable dynamics.
For water, a more challenging system, the timestep has to be reduced to 1fs. The BDP approach is more efficient than Nose-Hoover for small and large values of the time scale of the thermostat. For moderate values, the two approaches agree well. They also show that dynamic properties of the system can be calculated by finding the vibrational spectrum of ice 1h at 120K (using a smaller timestep of 0.5fs). Two very different values of the time scale give essentially identical spectra, which also agree with the micro-canonical results. The diffusion coefficient of water is also well calculated, only showing significant errors for very small values of the time scale.
Overall, this new thermostat appears to be both efficient and robust. It obeys ergodicity, samples the canonical ensemble and could be extended to allow constant pressure simulations. The authors have suggested a way to monitor the quality of numerical integration which involves the accuracy of sampling rather than the accuracy of trajectories. This makes the monitor applicable to all stochastic methods, which will benefit from a simple way to check errors introduced by numerical integration.
 J. Chem. Phys. 126, 014101 (2007) DOI: 10.1063/1.2408420