Each system was then energy minimized with 2000 steps of CG, gradually heated to 300 K over 30 ps, and followed by an equilibration step of 1 ns in NPT condition and maintained at 1 atm and 300 K, using the Langevin barostat and thermostat, respectively. The average size of the box was calculated and a production run of 30 ns was performed in NVT condition at 300 K, using the Langevin thermostat. To improve convergence, production runs were extended to 100 ns for streptavidin, hivpr, and nram, and to 200 ns for fabp4 protein. Conformations were saved every 1000 steps (i.e., 2 ps) for the subsequent analysis. Finally, MD simulations were repeated for each system to generate 3 replicate trajectories.