Skip to main content Accessibility help
×
Home

Molecular Dynamics Simulations of a Siloxane-Based Liquid Crystal Using an Improved Fast Multipole Algorithm Implementation

  • Alan McKenney (a1), Ruth Pachter (a1), Soumya Patnaik (a1) and Wade Adams (a1)

Abstract

In our continuing efforts towards designing materials with controlled optical properties, largescale molecular dynamics simulations of a molecular cluster of a liquid crystalline cyclic siloxane are still limited by the size of the molecular system. Such simulations enable evaluation of the orientation order parameter of the system, as well as modelling the behavior of the material in bulk. This study summarizes improvements in the implementation of the fast multipole algorithm for computing electrostatic interactions which is included in the molecular dynamics program PMD[7, 8], such as the elimination of computations for empty cells and the use of optimal interaction lists. Moreover, an improved implementation of a 3-D Fast Multipole Method (FMM3D) based on the algorithm previously proposed[1, 2] is described in detail. The structure of the module, details of the expansions, parallelization, and its integration with the molecular dynamics simulation code are explained in detail. Finally, the utility of this approach in the study of liquid crystalline materials is briefly illustrated.

Copyright

References

Hide All
1. Greengard, L. and Rokhlin, V., Rapid evaluation of potential fields in three dimensions, in Vortex Methods, edited by Anderson, C. and Greengard, C., volume 1360 of Lecture Notes in Mathematics, pages 121141, Berlin, 1988, Springer Verlag.
2. Greengard, L. and Rokhlin, V., On the efficient implementation of the fast multipole algorithm, Technical Report YALEU/DCS/RR-602, Yale University Dept. of Computer Science, 1988.
3. Guenot, J. and Kollman, P. A., Journal of Computational Chemistry 14, 295 (1993).
4. Grubmüller, H., Heller, H., Windemuth, A., and Schulten, K., Molecular Simulation 6, 121 (1991).
5. Brooks, B. R. et al., Journal of Computational Chemistry 4, 187 (1983).
6. Greengard, L. and Rokhlin, V., J. Comp. Physics 73, 325 (1987).
7. Windemuth, A. and Schulten, K., Molecular Simulation 5, 353 (1991), (Reference not verified).
8. Board, J. A. Jr., Causey, J. W., Leathrum, J. F. Jr., Windemuth, A., and Schulten, K., Chem. Phys. Letters 198, 89 (1992).

Metrics

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed