Which software you are using for MD simulation study and what type of system you have considered?
If it is Gromacs, just you have to use "gmx g_energy" command and select protein. After selecting the protein, all the energy function name will appear on your working terminal then you have to select mention serial number of that energy function. you will get energy as well as the plot of that energy with respect to time/frame.
Nandan Kumar, gmx g_energy does not give any option for choosing the protein. I can choose kinetic energy for whole system (protein+water) not only protein