Fandom

VroniPlag Wiki

Ry/Fragment 053 01

< Ry

31.340Seiten in
diesem Wiki
Seite hinzufügen
Diskussion1 Share

Störung durch Adblocker erkannt!


Wikia ist eine gebührenfreie Seite, die sich durch Werbung finanziert. Benutzer, die Adblocker einsetzen, haben eine modifizierte Ansicht der Seite.

Wikia ist nicht verfügbar, wenn du weitere Modifikationen in dem Adblocker-Programm gemacht hast. Wenn du sie entfernst, dann wird die Seite ohne Probleme geladen.


Typus
KomplettPlagiat
Bearbeiter
Klgn
Gesichtet
Yes.png
Untersuchte Arbeit:
Seite: 53, Zeilen: 1 ff. (entire page)
Quelle: Anézo 2003
Seite(n): 70, 71, Zeilen: 70:20-32; 71: 1-14
[LINCS is a more stable and efficient constraint algorithm, which allows time steps of at] least 3–4 fs. LINCS can be easily parallelized and is three or four times faster than SHAKE at the same accuracy.

Another alternative to relieve the limitation related to the sampling of the fast degrees of freedom is the implementation of multiple time step (MTS) integrators [58]. The various forces present in the system are separated into several components according to their characteristic time scales. The equations of motion involving the fast components are integrated with a small time step, whereas a longer time step is used to handle slow motions. These results decrease the CPU time in the simulation.

II.2.6 Treatment of long-range interactions

The membrane system is a very large and flexible system in which all components are tightly packed together and the bilayer structure is maintained only by the non-bonded interactions. The treatment of these non-bonded interactions in a simulation requires thus special care. While van der Waals interactions rapidly decrease with increasing distance (fast decline of the Lennard-Jones potential), Coulomb interactions are quite long-ranged. The correct handling of long-range electrostatic interactions in phospholipid bilayers is of particular concern since the headgroups of many phospholipids are highly charged or contain strongly polar groups. The most straightforward way of calculating electrostatic interactions would be to simply evaluate the Coulomb interactions between each pair of charged atoms in the system. In the simulation of large systems like membranes, the computation of electrostatics constitutes one of the most expensive tasks and the computational cost to include all atom pair interactions is prohibitive. To reduce computational effort, approximations have to be introduced into the calculation of the long-range electrostatic contribution. Since these approximations often belong to the most drastic ones in a simulation procedure, they are expected to have a significant influence on the system structure and dynamics and, for this reason, need to be applied with care. The most common techniques used for the treatment of electrostatics are briefly surveyed below.


58. Cheng, A.; Jr., K. M. M. J. Phys. Chem. B 1999, 103, 5396.

[page 70]

LINCS is a more stable and efficient constraint algorithm which allows time steps of at least 3–4 fs. LINCS can be easily parallelized and is three or four times faster than SHAKE at the same accuracy.

Another alternative to relieve the limitation related to the sampling of the fast degrees of freedom is the implementation of multiple time step (MTS) integrators [110]. The various forces present in the system are separated into several components according to their characteristic time scales. The equations of motion involving the fast components are integrated with a small time step, whereas a longer time step is used to handle slow motions. This results in a significant decrease of CPU time in the simulation.

3.2.2.6 Treatment of long-range interactions

The membrane system is a very large and flexible system in which all components are tightly packed together and the bilayer structure is maintained only by the non-bonded interactions. The treatment of these non-bonded interactions in a simulation requires thus special care.

[page 71]

While van der Waals interactions rapidly decrease with increasing distance (fast decline of the Lennard-Jones potential), Coulomb interactions are quite long-ranged. The correct handling of long-range electrostatic interactions in phospholipid bilayers is of particular concern since the headgroups of many phospholipids are highly charged or contain strongly polar groups. The most straightforward way of calculating electrostatic interactions would be to simply evaluate the Coulomb interactions between each pair of charged atoms in the system. In the simulation of large systems like membranes, the computation of electrostatics constitutes one of the most expensive tasks and the computational cost to include all atom pair interactions is prohibitive. To reduce computational effort, approximations have to be introduced into the calculation of the long-range electrostatic contribution. Since these approximations often belong to the most drastic ones in a simulation procedure, they are expected to have a significant influence on the system structure and dynamics and, for this reason, need to be applied with care. The most common techniques used for the treatment of electrostatics are briefly surveyed below.


[110] A. Cheng and K. M. Merz Jr. J. Phys. Chem. B, 103:5396–5405, 1999.

Anmerkungen

The source is not given.

Sichter
(Klgn), WiseWoman

Auch bei Fandom

Zufälliges Wiki