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Typus
KomplettPlagiat
Bearbeiter
WiseWoman
Gesichtet
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Untersuchte Arbeit:
Seite: 54, Zeilen: 1 ff. (entire page)
Quelle: Anézo 2003
Seite(n): 71-72, Zeilen: 71:16-33; 72: 1-13
Truncation techniques. One of the most frequently used techniques applied in biomolecular simulations to speed up the computations is truncation of the long-range electrostatic forces. These so-called cutoff methods are also widely used in membrane simulations. Interactions beyond a predefined maximum, the cutoff distance RC, are neglected to reduce the amount of time spent computing the large number of pairwise electrostatic interactions present in the simulated system. Such spherical cutoffs can be implemented in different ways, depending on whether the distance is calculated between the interacting atoms (atom based) or between groups of atoms (group-based). In the case of atom-based truncation, electrostatic interactions are computed for each atom pair within the cutoff sphere. Substantial distortions can however occur when the cutoff distance from an atom A includes one atom of a dipole B–C (i.e. B or C), but not the other. This gives rise to an exaggerated attraction between A and B–C and an artificial charge-dipole orientation of B–C relative to A. To eliminate such effects, the use of group-based cutoffs is recommended. Neighboring atoms are clustered into bonded charge groups, usually with no net charge. For any atom pair within the cutoff distance, all pair interactions between the corresponding charge groups are included in the electrostatic computation. This group-based method enables one to avoid the artificial creation of charges cutting through dipoles. When periodic boundary conditions are used, the minimum-image convention is generally applied to prevent double counting of the interactions between the atoms in the central simulation cell and those in the images: only one image of each particle (the nearest one) is considered for a pair interaction. To avoid that an atom interacts with its own image, the cutoff radius used to truncate the non-bonded interactions must not exceed half the box size (considering the shortest box vector in the case of non-cubic simulation boxes). To circumvent the abrupt truncation of the electrostatic interactions by a straight cutoff, “shift” or “switch” functions can be applied to smooth the interaction energy or force to zero, either within the whole cutoff range or over a limited region. The truncated forces are thus replaced by continuous forces, which have continuous derivatives at the cutoff radius. A shift function increases the magnitude of the force or potential before it is smoothed to zero (i.e. adds a function to the force or potential), while a switch function multiplies the force or potential by a function. There is actually no fundamental difference between both functions and the [switch function can be considered as a special case of the shift function.] Truncation techniques One of the most frequently used techniques applied in biomolecular simulations to speed up the computations is truncation of the long-range electrostatic forces. These so-called cutoff methods are also widely used in membrane simulations. Interactions beyond a predefined maximum, the cutoff distance RC, are neglected to reduce the amount of time spent computing the large number of pairwise electrostatic interactions present in the simulated system. Such spherical cutoffs can be implemented in different ways, depending on whether the distance is calculated between the interacting atoms (atom-based) or between groups of atoms (group-based). In the case of atom-based truncation, electrostatic interactions are computed for each atom pair within the cutoff sphere. Substantial distortions can however occur when the cutoff distance from an atom A includes one atom of a dipole B—C (i.e. B or C), but not the other. This gives rise to an exaggerated attraction between A and B—C and an artificial charge-dipole orientation of B—C relative to A. To eliminate such effects, the use of group-based cutoffs is recommended. Neighboring atoms are clustered into bonded charge groups, usually with no net charge. For any atom pair within the cutoff distance, all pair interactions between the corresponding charge groups are included in the electrostatic computation. This group-based method enables one to avoid the artificial creation of charges cutting through dipoles. When periodic boundary conditions are used, the minimum-image convention is generally applied to prevent double

[page 72]

counting of the interactions between the atoms in the central simulation cell and those in the images: only one image of each particle (the nearest one) is considered for a pair interaction. To avoid that an atom interacts with its own image, the cutoff radius used to truncate the non-bonded interactions must not exceed half the box size (considering the shortest box vector in the case of non-cubic simulation boxes). To circumvent the abrupt truncation of the electrostatic interactions by a straight cutoff, “shift” or “switch” functions can be applied to smooth the interaction energy or force to zero, either within the whole cutoff range or over a limited region. The truncated forces are thus replaced by continuous forces which have continuous derivatives at the cutoff radius. A shift function increases the magnitude of the force or potential before it is smoothed to zero (i.e. adds a function to the force or potential), while a switch function multiplies the force or potential by a function. There is actually no fundamental difference between both functions and the switch function can be considered as a special case of the shift function.

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