Dear Gromacs users,
I have performed a Molecular Dynamics-Simulated Annealing protocol with the goal to find the global minimum (cooling to 0 K) of the energy landscape for a small molecule in water environment. My question is what could I do next to find this global minimum?
It would be enough to just analyze the total energy of each frame of the trajectory or it would be better to do some kind of clustering analysis or perform dihedral principal components analysis to visualize the free energy landscape of the trajectory and extract the frames in the bin with the lowest energy?
Would appreciate any directions