calculating rmse from estimates with different interval spacing

I would like to calculate the rmse between an observation and a model result estimate. The matrix dimensions are not the same for both matrices. is there a way to do this in matlab?

[the cyclist]

Probably, but you need to add more detail about your observations and model results are stored, and what you know about how to match up the two up.

Ideally, provide the actual vectors (or simplified examples), rather than just descriptions.