GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: No
I am trying to measure the free energy of two docked proteins [protein-protein] system. I have already performed the MD simulation and now trying to measure the energy.
I am have searched online to learn how to perform the calculations using MM/PBSA and/or MM/GBSA but all I could find are tutorials and tools for [protein-ligand] systems, and I am not sure how to modify these programs to work for a [protein-protein] system.
Anyone can guide me on where to find the relevant information? and how to perform the calculation? is there an algorithm that is part of the gmx suit?