Gromacs

Blowing Up

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    Version as of 15:42, 30 Nov 2021

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    "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.

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

    Page last modified 14:16, 8 Oct 2009 by JLemkul?