The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: How well is the x‐ray structure “maintained”?

We present molecular dynamics simulations on ubiquitin with explicit solvent molecules and investigate the influence of different force fields [Weiner et al. (J. Am. Chem. Soc. 106:765–784, 1984; J. Comput. Chem. 7:230–252, 1986) vs. Cornell et al. (J. Am. Chem. Soc. 117:5179–5197, 1995)], different treatments of the long‐range electrostatic interaction (8 Å cutoff vs. particle mesh Ewald), and different solvation models (periodic box vs. small shell of water molecules) on the structure and the dynamics of the protein. Structural data are monitored by atomic root mean square deviations (RMSDs) from the crystal structure, the radius of gyration, the solvent‐accessible surface area, and the pattern of the backbone hydrogen bonds. The dynamic behavior is assessed by the atomic fluctuations and the order parameters of the N‐H backbone vectors.