THE CONSISTENCY OF LARGE CONCERTED MOTIONS IN PROTEINS IN MOLECULAR-DYNAMICS SIMULATIONS

A detailed investigation is presented into the effect of limited sampl ing time and small changes in the force field on molecular dynamics si mulations of a protein. Thirteen independent simulations of the B1 IgG -binding domain of streptococcal protein G were performed, with small changes in the simulation parameters in each simulation, Parameters st udied included temperature, bond constraints, cut-off radius for elect rostatic interactions, and initial placement of hydrogen atoms, The es sential dynamics technique was used to reveal dynamic differences betw een the simulations. Similar essential dynamics properties were found for all simulations, indicating that the large concerted motions found in the simulations are not particularly sensitive to small changes in the force field, A thorough investigation into the stability of the e ssential dynamics properties as derived from a molecular dynamics simu lation of a few hundred picoseconds is provided. Although the definiti on of the essential modes of motion has not fully converged in these s hort simulations, the subspace in which these modes are confined is fo und to be reproducible.