Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides. The reaction field method.
In this paper we present a model system of a solvated polypeptide, which is a suitable reference platform for the systematic exploration of methods for taming artifacts introduced by an incorrect treatment of long-range Coulomb forces. The essential feature of the system composed of an alpha-helical peptide and 1021 water molecules is the strict neutrality of all charge groups. The dynamical properties of the peptide, i.e. unfolding or maintenance of the helix, already give first hints on the influence of boundary effects. A rigorous and deeper insight is gained, however, if analyzing the system by means of the generalized Kirkwood g-factor, which projects the net dipole moment of concentric spheres onto the respective dipole moment of the reference charge group. The g-factor is a global measure for, and a sensitive probe of, the orientational structure, which in its turn reflects even the smallest inconsistencies in the treatment of long-range forces. While the cut-off scheme failed the g-factor test, the "reaction field" method, the simplest cut-off correction scheme, enables a consistent description. In other words, with the aid of the reaction field, the correct orientational structure is restored. As a consequence, the helix stability is regained and we were able to calculate the dielectric constant epsilon approximately 55 to 60 for our system, which is slightly below the corresponding value epsilon SPC = 66 of the pure solvent.
Schreiber
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H
Institute for Theoretical Chemistry, Molecular Dynamics Group, Vienna, Austria.
Steinhauser
O
O
D000595:Amino Acid Sequence; D016477:Artifacts; D004560:Electricity; D008432:Mathematical Computing; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009038:Motion; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012984:Software; D012996:Solutions / Q000737:chemistry
D010455:Peptides; D012996:Solutions