Multiple multipole method

Fig. 3.18. Normalized differential scattering cross-sections of an oblate cylinder with ksb = 15 and 2ksa = 7.5. The cmves are computed with the TAXSYM routine, discrete somces method (DSM), multiple multipole method (MMP), discrete dipole approximation (DDA) and finite integration technique (CST)...

Fig. 3.50. Normalized differential scattering cross-sections of a system of two prolate spheroids computed with the TMULT routine and the multiple multipole method (MMP)...

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

As an example for an efficient yet quite accurate approximation, in the first part of our contribution we describe a combination of a structure adapted multipole method with a multiple time step scheme (FAMUSAMM — fast multistep structure adapted multipole method) and evaluate its performance. In the second part we present, as a recent application of this method, an MD study of a ligand-receptor unbinding process enforced by single molecule atomic force microscopy. Through comparison of computed unbinding forces with experimental data we evaluate the quality of the simulations. The third part sketches, as a perspective, one way to drastically extend accessible time scales if one restricts oneself to the study of conformational transitions, which arc ubiquitous in proteins and are the elementary steps of many functional conformational motions. 

In general, multiple-time-step methods increase computational efficiency in a way complementary to multipole methods The latter make use of regularities in space, whereas multiple-time-stepping exploits regularities in time. Figure 2 illustrates the general idea ... 

Higher-order multipole moments enhance the forces between particles at short distances and their neglect is extremely questionable, especially if fine effects are looked at, as for instance the ground-state properties of close-packed lattice structures [244,246-251] or the viscosity To go beyond the point dipole approximation Klingenberg and co-workers [ 173,252] developed an empirical force expression for the interaction between two dielectric spheres in a uniform external field from the munerical solution of Laplace s equation [253]. Recently, Yu and co-workers [254,255] proposed a computationally efficient (approximate) dipole-induced-dipole model based on a multiple image method which accounts partially for multipolar interactions. 

The fifth and final chapter, on Parallel Force Field Evaluation, takes account of the fact that the bulk of CPU time spent in MD simulations is required for evaluation of the force field. In the first paper, BOARD and his coworkers present a comparison of the performance of various parallel implementations of Ewald and multipole summations together with recommendations for their application. The second paper, by Phillips et AL., addresses the special problems associated with the design of parallel MD programs. Conflicting issues that shape the design of such codes are identified and the use of features such as multiple threads and message-driven execution is described. The final paper, by Okunbor Murty, compares three force decomposition techniques (the checkerboard partitioning method. 

Schulten238 outlined the development of a multiple-time-scale approximation (distance class algorithm) for the evaluation of nonbonded interactions, as well as the fast multipole expansion (FME). efficiency of the FME was demonstrated when the method outperformed the direct evaluation of Coulomb forces for 5000 atoms by a large margin and showed, for systems of up to 24,000 atoms, a linear dependence on atom number. 

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