Blowing Up

"Blowing up" is a highly technical term used to describe a common sort of simulation failure. In brief, it describes a failure typically due to an unacceptably large force that ends up resulting in a failure of the integrator.

To give a bit more background, it's important to remember that molecular dynamics numerically integrates Newton's equations of motion by taking small, discrete timesteps, and using these timesteps to determine new velocities and positions from velocities, positions, and forces at the previous timestep. If forces become too large at one timestep, this can result in extremely large changes in velocity/position when going to the next timestep. Typically, this will result in a cascade of errors: one atom experiences a very large force one timestep, and thus goes shooting across the system in an uncontrolled way in the next timestep, overshooting its preferred location or landing on top of another atom or something similar. This then results in even larger forces the next timestep, more uncontrolled motions, and so on. Ultimately, this will cause the simulation package to crash in some way, since it can't cope with such situations. In simulations with constraints, the first symptom of this will usually be some LINCS or SHAKE warning or error -- not because the constraints are the source of the problem, but just because they're the first thing to crash. Similarly, in simulations with domain decomposition, you may see messages about particles being more than a cell length out of the domain decomposition cell of their charge group, which are symptomatic of your underlying problem, and not the DD algorithm itself. This can happen on one computer system while another resulted in a stable simulation because of the impossibility of numerical reproducibility of these calculations on different computer systems.

Possible causes include:

• you didn't minimize well enough,
• you have a bad starting structure, perhaps with steric clashes,
• you are using too large a timestep (particularly given your choice of constraints),
• you are doing particle insertion in free energy calculations without using soft core,
• you are using inappropriate pressure coupling (e.g. when you are far from equilibrium, Berendsen can be best for fixing the volume, but you will need to switch to a more accurate pressure-coupling algorithm later),
• you are using inappropriate temperature coupling, perhaps on inappropriate groups, or
• you have a single water molecule somewhere within the system that is isolated from the other water molecules.

Because blowing up is due, typically, to forces that are too large for a particular timestep size, there are a couple of basic solutions:

1. Make sure the forces don't get that large, or
2. use a smaller timestep.

Better system preparation can help with 1, if the problems are occurring near the beginning of a simulation.