# Ry/Fragment 039 01

## < Ry

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 Typus Verschleierung Bearbeiter Klgn Gesichtet
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Seite: 39, Zeilen: 1-22
Quelle: Anézo 2003
Seite(n): 62, 56, 57, Zeilen: 62: 2 ff; 56:28-29; 57: 1-4
[This introduces the problem of combining the right conditions and parameters in order to] obtain a correct bilayer model system, such simulation conditions being indeed an integral part of the model.

II.2.2 Force fields

The choice of interatomic force fields and related parameters is of crucial importance for the simulation of a biomolecular system. The ability of a model membrane to reproduce realistic static and dynamic features depends strongly on the balance between attractive and repulsive forces, which directly results from the force field employed. A force field is indeed required to compute the potential energy of the system as a function of the instantaneous atomic coordinates. Various force fields have been developed to simulate proteins and nucleic acids; no special force fields have however been designed for the modeling of lipid bilayers. With the exception of charges, which are often derived from ab initio quantum chemical calculations on lipid fragments, the parameters in the potential functions are thus usually taken from pre-existing force fields for proteins or nucleic acids. The most popular force fields used in membrane simulation studies are the AMBER [46], the CHARMM [47], and the GROMOS [48] force fields. One of these force fields is often applied in combination with the OPLS (Optimized Potentials for Liquid Simulations) [49] parameter set for the computation of the non-bonded interactions.

All necessary information for system description is contained in the potential V, which is derived from the force field. The force field can be defined as set of equations (potential functions) and parameters, which characterize interactions into the system. Both components are interdependent.

46. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765.

47. Brooks, B. R.; R. E. Bruccoleri; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comp. Chem. 1983, 4, 187.

48. Gunsteren, W. F. v.; Berendsen, H. J. C. Groningen Molecular Simulation (GROMOS) Library Manual; Biomos: Groningen, The Netherlands, 1987.

49. Schlenkrich, M.; Brickman, J.; Jr., A. D. M.; Karplus, M. An Empirical Potential Energy Function for Phopholipids: Criteria for Parameter Optimization and Applications. In Biological Membranes: A Molecular Perspective from Computation and Experiment; Jr., K. M. M., Roux, B., Eds.; Birhдuser [sic]: Boston, 1996.

[page 62]

This introduces the problem of combining the right conditions and parameters in order to obtain a correct bilayer model system, such simulation conditions being indeed an integral part of the model.

3.2.2.1 Force fields

The choice of interatomic force fields and related parameters is of crucial importance for the simulation of a biomolecular system. The ability of a model membrane to reproduce realistic static and dynamic features depends strongly on the balance between attractive and repulsive forces, which directly results from the force field employed. A force field is indeed required to compute the potential energy of the system as a function of the instantaneous atomic coordinates. Various force fields have been developed to simulate proteins and nucleic acids; no special force fields have however been designed for the modeling of lipid bilayers [44]. With the exception of charges, which are often derived from ab initio quantum chemical calculations on lipid fragments, the parameters in the potential functions are thus usually taken from pre-existing force fields for proteins or nucleic acids. The most popular force fields used in membrane simulation studies are the AMBER [86], the CHARMM [87], and the GROMOS [88] force fields. One of these force fields is often applied in combination with the OPLS (Optimized Potentials for Liquid Simulations) parameter set [89] for the computation of the non-bonded interactions. [...]

[page 56]

[...] All the information necessary to describe the system simulated is contained in the interaction potential V, which is a function of the underlying force field. A force field can be

[page 57]

defined as a set of equations (potential functions) on the one hand, and parameters on the other hand, characterizing the strength of the various interactions within the system. Both components – potential functions and parameters used in these functions – are however interdependent and are combined to form a consistent set.

[44] M. Wiese. Computer Simulation of Phospholipids and Drug-Phospholipid Interactions. In: Drug-Membrane Interactions. J. K. Seydel and M. Wiese (Eds.), Wiley- VCH Verlag GmbH, Weinheim, 2002.

[86] S. J.Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner. J. Am. Chem. Soc., 106:765–784, 1984.

[87] B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. J. Comput. Chem., 4:187–217, 1983.

[88] W. F. van Gunsteren and H. J. C. Berendsen. Groningen Molecular Simulation (GROMOS) Library manual. Biomos, Nijenborgh 4, 9747 AG Groningen, The Netherlands, 1987.

[89] W. Jorgensen and J. Tirado-Rives. J. Am. Chem. Soc., 110:1666–1671, 1988.

[90] M. Schlenkrich, J. Brickmann, A. D. MacKerell Jr., and M. Karplus. An Empirical Potential Energy Function for Phospholipids: Criteria for Parameter Optimization and Applications. In: Biological Membranes: A Molecular Perspective from Computation and Experiment. K. M. Merz Jr. and B. Roux (Eds.), Birhäuser, Boston, 1996.

 Anmerkungen No source is given. The Russian letter д instead of ä is found twice in the thesis. This happens when copy & pasting with a Cyrillic keyboard. Reference 49. in Ry is reference [90] in the source, not [89]. Sichter (Klgn), WiseWoman