Model Development And Results

The molecular dynamics method is well known and has been reviewed in several papers.1112 Basically one needs to solve Hamilton's equations, or any other formulation ofthe classical equations ofmotion, starting from some initial positions and momenta ofall ofthe atoms in the system and propagating the solution in a series oftime steps. In our MD simulations, the integrations ofthe equations of motion are carried out in Cartesian coordinates, thus giving an exact definition of the kinetic energy and coupling. The classical equations of motion are formulated using our geometric statement function approach,13 which significantly reduces the number of mathematical operations required. These coupled equations are solved using novel symplecticintegrators developed in our laboratory which conservethe volume ofphase space and robustly allow integration for virtually any time scale.14

Molecular Hamiltonian and Potential Energy Functions

For simplicity, the united atom PE modelwas used in which the CH2 and CH3 groups are treated as a single particle (bead) ofmass m = 14.5 amu. By neglecting the internal structure of those groups, we reducethe number ofequations ofmotion for the system and save a significant amount of computational time. The MD simulations compute the momenta and coordinate of

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