Fig. 3
From: StreaMD: the toolkit for high-throughput molecular dynamics simulations
Correlation between calculated MM-GBSA free energies and observed pKd (Pearson R = −0.69) for 624 protein–ligand complexes from the Greenidge data set [14]. Free energies were calculated from the last 5 ns of the trajectories using each fifth frame and internal dielectric constant 4. Red dots are compounds which have not converged trajectories: average RMSD > 5 Å or standard deviation of RMSD > 0.5 Å