Grid-based dynamic electronic publication: A case study using combined experiment and simulation studies of crown ethers at the air/water interface.
Esther R Rousay, Hongchen Fu, Jamie M Robinson, Jeremy G Frey, Jonathan W Essex
School of Chemistry, University of Southampton,
Highfield, Southampton, SO17 1BJ, UK

Abstract The Publication@Source Paradigm and Challenges Body Molecular Dynamics Simulations Comparisons and Conclusions Acknowledgements Appendix:The TriScapeRDF browser References Glossary Search
Introduction Introduction - Compute Facility Figures Density Profiles Orientational Distribution

Orientational Distribution

Plotting the distribution of the tilt angle cosines (figure 12 b) shows that the chromophore is hydrophobic, and the weakly preferred average tilt angle is about 74o to the surface normal. Calculating the order parameters for each frame, and averaging over the whole 10 ns simulation gives 〈P1〉=0.237 and 〈P3〉 = -0.084. The D parameter calculated through SHG can be expressed in terms of the Legendre polynomials of Θtilt:

D = (2〈P3〉+3〈P1〉) / 5〈P1

Evaluating this equation for the 10 ns simulation resulted in a value of D = 0.458. This differs from the experimental value, which is close to the weak limit33 an alternative way to view this is to consider the value of <P3>, which tends to zero in the weak limit.

Figure 12. The normalised distributions of the tilt angles, left hand plot, and the cosines of the tilt andles, over the simlation for each chromophore.

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