Dear Drea,

To calculate the interaction energy, U can perform the MD simulation and then MMPBSA calculation or u can perform the QM/MM calculation of ur complex to calculate the interaction energy.

MD Simulation using Gromacs:

http://www.gromacs.org/Documentation/Terminology/Molecular_Dynamics_Simulations

Gromacs Tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/

MMPBSA Tutorial:

http://rashmikumari.github.io/g_mmpbsa/Tutorial.html

Regards,

Nandan