I’m not sure about VPI, but this is definitely something you could do in OptiSystem. The best way to go about it would depend on exactly what you want to investigate. Do you want to calculate the time delay of the entire signal after propagating through the fiber or are you interested in some phase delay between different modes? The first result could be found simply from the Clock Recovery component and the second could be retrieved from the Differential Mode Delay component.
Cheers