Atomistic molecular dynamics (MD) simulations were performed in CHARMM , using CHARMM 36 force field  to further relax homology models and to investigate secondary structure and dynamics of the tag-less MEFA protein. Protein model was first solved in a cubic box of TIP3P water , and the total protein charge was neutralized by adding sodium ions. The final box size was about 69 Å. After energy minimization, 5.0 ns (nanosecond) simulation was used to equilibrate the structure by gradually reducing the harmonic positional restrain imposed on the protein backbone. The final production simulation course lasted 350 ns. Langevin dynamics  were performed at a constant temperature of 298 K and pressure of 1.0. SHAKE algorithm  was applied to maintain the length of all hydrogen-containing bonds and to allow of 2.0 fs (femto second) timestep. Particle mesh Ewald  was utilized for electrostatics with a real-space cutoff of 13 Å. Van der Waals interactions were gradually switched off between 12 Å and 13 Å.