Hello,
I am simulating 100 protein-protein complex over 30 ns or until converged. Therefore the time used for mmgbsa analysis with nmode every 5ns from convergence time, vary between different complex. For instance, I might use 40-60 ns for one structure and 20-30 ns for another. Please let me know if the final results can be generalised or the different time for analysis might result in inaccuracy?