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KomplettPlagiat
Bearbeiter
WiseWoman
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Untersuchte Arbeit:
Seite: 55, Zeilen: 1 ff (entire page)
Quelle: Anézo 2003
Seite(n): 72, Zeilen: 72: 13 ff.; 73: 1-7
Truncation of the long-range electrostatic interactions may introduce serious artifacts into computer simulations. The artifacts caused by the use of cutoffs have generally been attributed to a net ordering in the vicinity of the cutoff radius.

Ewald summation techniques. One way to eliminate truncation effects is to include all the electrostatic interactions in the infinite array of periodic replicas of the central simulation cell by using Ewald summation techniques. Applying such techniques, electrostatic interactions are in principle considered with an infinite cutoff. The Ewald summation has originally been developed to handle long-range electrostatic interactions in simulations carried out with periodic boundary conditions and has traditionally been used to compute electrostatics in crystals. This method can be however applied to other systems, provided the charges in the system are distributed over a fine grid. The Ewald summation technique is nonetheless very costly from a computational point of view and has rarely been used for systems as large as lipid bilayers. Improved algorithms based on simplifications of the Ewald sum, like the Particle-Particle Particle-Mesh (P3M) method [59] or the Particle-Mesh Ewald (PME) method [60,61], have been developed for a more rapid and efficient convergence of the Ewald equations, and have been applied with success in numerous membrane simulations. The current trend to take long-range electrostatic interactions explicitly into account via Ewald techniques is certainly done in an exact but periodical manner, so that artificial periodicity may be enhanced. While periodic boundary conditions already introduce a factitious periodicity into the system, Ewald summation techniques include this periodicity at all times in the long-range electrostatic interactions. Whether or not such effects are significant is obviously dependent on the system size and the properties of interest.

Reaction field approach. An alternative method that incorporates the full electrostatic interactions is the reaction field approach, in which the Coulomb potential is corrected for the effect of the polarizable surroundings beyond the cutoff radius. This method has been developed for homogeneous systems, for instance for liquid simulations, or for a small solute immersed in a solvent.


59. Hockney, R. W.; Eastwood, J. W. Computer Simulation using Particles; McGraw-Hill: New York, 1981.

60. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.

61. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089.

Truncation of the long-range electrostatic interactions may introduce serious artifacts into computer simulations. The artifacts caused by the use of cutoffs have generally been attributed to a net ordering in the vicinity of the cutoff radius.

Ewald summation techniques One way to eliminate truncation effects is to include all the electrostatic interactions in the infinite array of periodic replicas of the central simulation cell by using Ewald summation techniques. Applying such techniques, electrostatic interactions are in principle considered with an infinite cutoff. The Ewald summation has originally been developed to handle long-range electrostatic interactions in simulations carried out with periodic boundary conditions and has traditionally been used to compute electrostatics in crystals. This method can be however applied to other systems, provided the charges in the system are distributed over a fine grid. The Ewald summation technique is nonetheless very costly from a computational point of view and has rarely been used for systems as large as lipid bilayers. Improved algorithms based on simplifications of the Ewald sum, like the Particle-Particle Particle-Mesh (P3M) method [111] or the Particle-Mesh Ewald (PME) method [112, 113], have been developed for a more rapid and efficient convergence of the Ewald equations, and have been applied with success in numerous membrane simulations. The current trend to take long-range electrostatic interactions explicitly into account via Ewald techniques is certainly done in an exact but periodical manner, so that artificial periodicity may be enhanced. While periodic boundary conditions already introduce a factitious periodicity into the system, Ewald summation techniques include this periodicity at all

[page 73]

times in the long-range electrostatic interactions. Whether or not such effects are significant is obviously dependent on the system size and the properties of interest (see Appendix B).

Reaction field approach An alternative method that incorporates the full electrostatic interactions is the reaction field (RF) approach, in which the Coulomb potential is corrected for the effect of the polarizable surroundings beyond the cutoff radius [114]. This method has been developed for homogeneous systems, for instance for liquid simulations, or for a small solute immersed in a solvent.


[111] R. W. Hockney and J. W. Eastwood. Computer Simulation using Particles. McGraw- Hill, New York, 1981.

[112] T. Darden, D. York, and L. Pedersen. J. Chem. Phys., 98:10089—10092, 1993.

[113] U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. J. Chem. Phys., 103:8577—8593, 1995.

[114] I. G. Tironi, R. Sperb, P. E. Smith, and W. F. van Gunsteren. J. Chem. Phys., 102:5451—5459, 1995.

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