Proceedings of the Second CSNI Workshop on Iodine Chemistry by A C Vikis; OECD Nuclear Energy Agency. Committee on the PDF

By A C Vikis; OECD Nuclear Energy Agency. Committee on the Safety of Nuclear Installations.; Atomic Energy of Canada Limited.; Ontario Hydro

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There can also be hindered equilibration effects that have their origin in finite box size effects. For example, if the number of lipids on each side of the bilayer is taken to be of order 30 to 100, which is reasonable, a fluctuation in this number is not expected to occur in the simulation, because this would be too large an overall perturbation. Cooperative movements of many molecules at the same time, which occasionally may be necessary before equilibration is a fact, may also be very slow.

We will return to this point below. A typical MD simulation usually consists of two parts. The first part is an equilibration time (ca. 1 ns) starting with a reasonably accurate initial configuration (see, for example, Figure 4), which is followed by a production run. 40 PHYSICOCHEMICAL KINETICS AND TRANSPORT AT BIOINTERFACES Considering the relatively short equilibration phase, one should always be alert for possible artifacts that originate from the choice of the initial configuration of the system.

A. M. LEERMAKERS AND J. M. KLEIJN 31 overall structure are large. There are differences in hydrocarbon chain length, chain branching, number and position of unsaturated bonds, hydrophilic head group size, charge, etc. There may be other lipid components, such as cholesterol, modulating the physical properties of the bilayers. Most of all, there are proteins embedded into the bilayer or associated with it. The complexity of the biological membranes poses huge problems for the molecular modelling of these objects.

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Proceedings of the Second CSNI Workshop on Iodine Chemistry in Reactor Safety : Toronto, Canada, 1988 June 2-3 by A C Vikis; OECD Nuclear Energy Agency. Committee on the Safety of Nuclear Installations.; Atomic Energy of Canada Limited.; Ontario Hydro


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