Section 20.1.4. Conclusions

In the present molecular-dynamics simulation, fast convergence in energy, within about 100 ps, was observed. Other properties, such as dihedral-angle fluctuations and backbone atom-position fluctuations, converged on an intermediate timescale of hundreds of picoseconds. Root-mean-square deviations of the simulated protein molecules from the starting X-ray structure required of the order of 1 ns to reach a plateau. Longer simulations would be necessary to obtain convergence for all molecular properties. The convergence of quickly relaxing properties of the system, such as the energies, is not a reliable indicator of the degree of global convergence in such a molecular-dynamics simulation.

The GROMOS96 force field used in this simulation largely reproduces the secondary structure and the relative internal mobility of ubiquitin. The simulation does, however, overestimate the magnitude of the fluctuations in the most mobile regions of the protein. The different protein molecules were observed to translate and rotate relative to one another during this simulation. This indicates that the force field would not be able to reproduce the experimental melting temperature of this crystal under the conditions simulated.