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| Untersuchte Arbeit: Seite: 46, Zeilen: 7-30 |
Quelle: Anézo 2003 Seite(n): 63, Zeilen: 7 ff |
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| II.2.3 System size and boundary conditions
According to the size scale of a MD simulation, a real lipid membrane is of infinite size. Only patches of a few lipid molecules can be generally simulated. This corresponds to a truncation of the system and can introduce possible artifacts. Indeed, a lipid membrane in the fluid state behaves like a liquid crystal, exhibiting a continuous spectrum of normal mode frequencies and wavelengths for thermally induced fluctuations in thickness and curvature. A truncation of the system eliminates all wavelengths longer than the simulation box. Another problem induced by truncation is that the simulation system is surrounded by a vacuum, leading to so-called “edge effects” – the behavior of the molecules located at the boundaries deviates from that of the molecules in the center. In the case of a very large system, the number of boundary molecules would be small enough to be neglected. The simulation of such large systems is unfortunately not feasible presently, so that membrane models are usually restricted to relatively small samples consisting of a few hundreds of lipid molecules. In this case, about 40% of the lipids belong to the border region. The commonly used method to eliminate edge effects is the implementation of periodic boundary conditions (PBC), which ensure that the system does not have an abrupt border with vacuum. It is assumed that the simulated system is surrounded on all sides by an exact replica of itself to form an infinite lattice. Thus, when a molecule leaves one side of the system, an identical molecule enters through the opposite side at the same time and at the corresponding position. Interactions of a molecule with its surroundings are calculated from both the original box and the neighboring cells. PBC are generally employed in liquid state simulations for systems presenting a homogeneous character in terms of chemical or structural composition. PBC have been widely used in membrane [simulations, as they naturally emulate the effectively infinite extent of the membrane.] |
3.2.2.2 System size and boundary conditions
According to the size scale of a MD simulation, a real lipid membrane is of infinite size. Only patches of a few lipid molecules can be generally simulated. This corresponds to a truncation of the system and can introduce possible artifacts. Indeed, a lipid membrane in the fluid state behaves like a smectic liquid crystal, exhibiting a continuous spectrum of normal mode frequencies and wavelengths for thermally induced fluctuations in thickness and curvature. A truncation of the system eliminates all wavelengths longer than the simulation box. Another problem induced by truncation is that the simulation system is surrounded by a vacuum, leading to so-called “edge effects”: the behavior of the molecules located at the boundaries deviates from that of the molecules in the center. In the case of a very large system, the number of boundary molecules would be small enough to be neglected. The simulation of such large systems is unfortunately not feasible presently, so that membrane models are usually restricted to relatively small samples consisting of a few hundreds of lipid molecules. In this case, about 40% of the lipids belong to the border region. The commonly used method to eliminate edge effects is the implementation of periodic boundary conditions (PBC), which ensure that the system does not have an abrupt border with vacuum. It is assumed that the simulated system is surrounded on all sides by an exact replica of itself to form an infinite lattice. Thus, when a molecule leaves one side of the system, an identical molecule enters through the opposite side at the same time and at the corresponding position. Interactions of a molecule with its surroundings is calculated from both the original box and the neighboring cells. PBC are generally employed in liquid state simulations for systems presenting a homogeneous character in terms of chemical or structural composition. PBC have been widely used in membrane simulations, as they naturally emulate the effectively infinite extent of the membrane. |
The source is not given. |
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