In the two systems I have been working on, making the inner box smaller or larger improves docking results, the outer box remaining the same. How would this happen?

As with all complex numerical algorithms (even local minimizations),variations in the results will occur when the initial conditions (e.g., grid parameters, ligand conformation) of the docking job are altered. Generally such fluctuations are more pronounced for poor binders, where there isn't a strong basin of attraction. While for your two systems changing the inner box size improved results, this might not always be the case and with other systems the results might be a bit worse. Generally, more poses would be expected from the larger grid.

Keywords: grid box size, effect on output

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