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GPS vs Knotmeter
A GPS and a knotmeter are reading two completely different things. The former measures speed over the bottom, the latter speed through the water. The former is useful for navigation, the latter for optimizing performance. One can be calculated from the other if the current strength and direction (called set and drift) are known. Tide and current tables may be able to tell you the set and drift predicted at a particular time.
A GPS is subject to random fluctuations of as much as a knot depending on the time over which velocity is averaged and whether it''s a differential or WAAS model. There is no calibration adjustment. A knotmeter needs to be calibrated, but once done should be much more accurate than a GPS over the short term (assuming that one is interested in speed through the water).
Over 100 miles, a GPS will average within .05% of the average speed over the ground for the journey. That''s because the GPS knows the starting and ending points, and the time taken, with an incredible degree of accuracy. A knotmeter will never do as well over a long distance: .05% of 6 knots is .003 knots, no knotmeter I know of reads to a resolution of less than .01 knots, and the accuracy is unlikely to be anything close to .01 knots.