# Ry/Fragment 057 01

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[With the continuous increase in computer speed and the improvement of the actual computational algorithms, time scales and system sizes will be enhanced by at least one order of magnitude in the] near future and one can expect that MD simulations of lipid bilayers will reach microsecond capabilities in the future.

The accuracy of a MD simulation is also limited by the accuracy of the underlying force field. The potential function used to describe the interactions in the simulated system is a simplified approximation of the “real” function and involves uncertain parameters like partial charges, Lennard-Jones constants, equilibrium values for bonds, angles and dihedrals, and force constants. In the commonly used force fields, atomic polarizability is furthermore omitted: average effects of polarizability are retained in the force field parameters, but detailed effects are not properly represented. Another crude approximation done in MD simulations is to compute only forces between pairs of atoms: three or four particle interactions are indeed neglected. To speed up calculations, long-range electrostatic interactions are often truncated beyond a given cutoff distance, which may have significant effects on the final results. Other methods have been implemented to include the long-range contribution, like Ewald summation or reaction field approaches. Each method has, however, some drawbacks, which have to be taken into account.

An extension of present computational algorithms and methodologies as well as a refinement of current force fields represent thus an important challenge in the MD field to gain both in efficiency and accuracy. Nevertheless, molecular dynamics still constitutes a very reliable technique to study structural and motional properties of biomolecular systems, as long as the limitations and approximations described above are not ignored and their influence on the results carefully is considered.

II.3. Permeation models

Two alternative models are commonly used to describe the molecular mechanisms of solute permeation through lipid membranes. One is referred as the solubility-diffusion model, in which the solute has to partition into and diffuse through the membrane. The other model, the defect model, involves the occurrence of transient pore-like defects such [as water pores in the lipid bilayer, which allow ions and small polar molecules to bypass the partitioning energy barrier.]

With the continuous increase in computer speed and the improvement of the actual computational algorithms, time scales and system sizes will be enhanced by at least one order of magnitude in the near future and one can expect that MD simulations of lipid bilayers will reach microsecond capabilities in the next five years.

The accuracy of a MD simulation is also limited by the accuracy of the underlying force field. The potential function used to describe the interactions in the simulated system is a simplified approximation of the “real” function and involves uncertain parameters like partial charges, Lennard-Jones constants, equilibrium values for bonds, angles and dihedrals, and force constants. In the commonly used force fields, atomic polarizability is furthermore omitted: average effects of polarizability are retained in the force field parameters, but detailed effects are not properly represented [116]. Another crude approximation done in MD simulations is to compute only forces between pairs of atoms: three or four particle interactions are indeed neglected. To speed up calculations, long-range electrostatic interactions are often truncated beyond a given cutoff distance, which may have significant effects on the final results. Other methods have been implemented to include the long-range contribution, like Ewald summation or reaction field approaches. Each method has, however, some drawbacks which have to be taken into account.

An extension of present computational algorithms and methodologies as well as a refinement of current force fields represent thus an important challenge in the MD field to gain both in efficiency and accuracy. Nevertheless, molecular dynamics still constitutes a very reliable technique to study structural and motional properties of biomolecular systems, as long as the limitations and approximations described above are not ignored and their influence on the results carefully is considered.

[page 139]

5.2.1 Permeation models

Two alternative models are commonly used to describe the molecular mechanisms of solute permeation through lipid membranes. One is referred as the solubility-diffusion model, in which the solute has to partition into and diffuse through the membrane. The other model, the defect model, involves the occurrence of transient pore-like defects such as water pores in the lipid bilayer which allow ions and small polar molecules to bypass the partitioning energy barrier.

[116] D. P. Tieleman, S. J. Marrink, and H. J. C. Berendsen. Biochem. Biophys. Acta, 1331:235―270, 1997.

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