If you run MD with amber, you can calculate the deta ASA with cpptray.

    Do three molsurf calculations: one with :1-290 (the first protein), one with :291-400(the second protein), and one with :1-400 (the complex). You get the deta ASA with the formula above. 

If you run MD with gromacs, you can use 

   gmx sasa [‐f [<.xtc/.trr/...>]] [‐s [<.tpr/.tpb/...>]] [‐n [<.ndx>]]

   [‐o [<.xvg>]] [‐odg [<.xvg>]] [‐or [<.xvg>]] [‐oa [<.xvg>]]

   [‐tv [<.xvg>]] [‐q [<.pdb>]] [‐b ] [‐e ] [‐dt ]

   [‐tu ] [‐xvg ] [‐[no]rmpbc] [‐[no]pbc] [‐sf ]

   [‐selrpos ] [‐probe ] [‐ndots ] [‐[no]prot]

   [‐dgs ] [‐surface ] [‐output ]

more details to see gromacs manual