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Figure 1 | BMC Bioinformatics

Figure 1

From: Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

Figure 1

Schematic showing the spatial binning of a periodic box and subsequent evaluation of atomic contacts in adjacent bins. a). Schematic showing the spatial binning of a periodic box. In this example, the protein (1enh, the engrailed homeodomain) is simulated in a periodic box of water molecules with dimensions of 50 Ã…. The periodic box is split into smaller boxes of 10 Ã… these are the 3 dimensional bins. For clarity the boxes in this figure are 10 Ã…, in our implementation we use box dimensions of 5.4 Ã…. Each bin is assigned an index and hence every atom at every time point will have associated X, Y, Z coordinates and a bin index. b) Schematic describing the evaluation of adjacent bins. To reduce the computational expense for detecting nearest neighbors one evaluates the atomic pair distance for atoms that are within the same bin and the immediately adjacent bins, shown by the cyan boxes. The white transparent sphere has a radius represented by the cutoff distance used as our criteria for the consideration of an atom to be in contact with the atom at the center of the sphere.

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