An FAQ question under HYSPLIT in General explains how to adjust the start height to account for differences between model terrain and actual terrain. I’m assuming that it’s most accurate to use actual elevation plus my desired trajectory height as a starting height, and specify the option KMSL=1 in the setup.cfg file on the PC. Is this correct? Occasionally these trajectories are wildly different from those with KMSL=0 and the start height specified as meters above ground level.
The choice of AGL or MSL depends upon the problem. My inclination would be to select a height above model terrain that is comparable to the height above actual terrain. In this way the physics of the planetary boundary layer are more accurately represented by the model calculation, regardless of the height of the actual terrain. That is why AGL is the model’s default option. However some people are interested in following the trajectory of a balloon which may have been started at a specific pressure level. Using the MSL option it is easier to start at a specific pressure level.