Gromacs

Average Structure

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    Various GROMACS utilities can compute average structures. Presumably the idea for this comes from something like an ensemble-average NMR structure. In some cases, it makes sense to calculate an average structure (as a step on the way to calculating root-mean-squared fluctuations, for example, one needs the average position of all of the atoms).

    However, it's important to remember that an average structure isn't necessarily meaningful. By way of analogy, suppose I alternate holding a ball in my left hand, then in my right hand. What's the average position of the ball? Halfway in between -- even though I always have it either in my left hand or my right hand. Similarly, for structures, averages will tend to be meaningless anytime there are separate metastable conformational states. This can happen on a sidechain level, or for some regions of backbone, or even whole helices or components of the secondary structure.

    Thus, if you derive an average structure from a molecular dynamics simulation, and find artifacts like unphysical bond lengths, weird structures, etc., this doesn't necessarily mean something is wrong. It just shows the above: an average structure from a simulation is not necessarily a physically meaningful structure.

    Page last modified 14:09, 8 Oct 2009 by JLemkul?