Molecular Dynamics - Stages and Duration of Dynamics Simulations

Dynamics simulations are usually carried out in two stages, equilibration and data collection. The duration of each stage depends on the system as well as on the properties under investigation.

The purpose of equilibration is to prepare the system so that it comes to the most probable configuration consistent with the target temperature and pressure. When a system is large, it may take a long time to equilibrate because of the vast conformational space it has to search. The contour of the energy surface is another factor to consider. If energy barriers between various local minima and the global minimum are high, barrier crossing is difficult and may take longer. One way to judge whether a system has equilibrated is to plot the various thermodynamic quantities, such as energy, temperature and pressure, versus time. When equilibration has been achieved, these quantities fluctuate around their averages, which remain constant over time. This is a necessary but not sufficient test, because it is not unusual for a sudden conformational change to occur after a long period of time. Another way to check equilibration is to start the calculation with different initial conformations and different initial velocities. Convergence to similar conformations and properties from different initial values is a good indicator that equilibration has occurred.

After preparing the system at the target temperature and pressure, you can begin collecting statistics. One commonly asked question is how long to collect the statistics. The answer depends on both the properties being calculated and the system being simulated. Some quantities, such as internal energy, temperature, and pressure, converge readily, since they are calculated from averages and the dominant contributions are from the most probable states. Other quantities, like specific heat or isothermal compressibilities, are more difficult to obtain, since they depend on the fluctuations. One empirical way to find out how long is long enough, is to monitor the change in these quantities over time.

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