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SITL not working with MATLAB... Plane not stable

Hi Guys, I am trying ardupliot simulation using Matlab and cygwin and displaying through mission planner. The input value for the cygwin is passed from Matlab. Initially, I am passing the values as zeros. But, pitch, roll and yaw angles are not taken as zero (44,-36,320 respectively, for example). This angles will change randomly when I restart the simulation. How do I calibrate to zero angles initially. Is it because of some mapping error? Please advise.

example for the above query

Servers by jDrones