Boxing algorithm

Represented as tolerance spheres, no explicit charges necessary Feature definitions as SMARTS or boxed algorithms, adjustment of feature specific parameters and geometric constraints... 

Similarity measures takes as input two schema elements, and it outputs a similarity between them. This similarity value may be a numerical value (e.g., a distance, a real in the range [0, 1]) or a relationship (e.g., equivalence, generalization). Similar to black-box algorithms, similarity measures can have internal parameters which impact the output. Due to the numerous available similarity measures, we do not intend to describe all of them with their parameters. Thus, we focus on two simple examples to illlustrate various types of such internal parameters. 

Based on observations concerning the dynamical behavior we already conjectured that there exist seven almost invariant sets - a conjecture that we now want to check numerically. We employ the subdivision algorithm for subtrajectories of length mr = 0.1. The final box-collection corresponding to the total energy E = 4.5 after 18 subdivision steps consists of 18963 boxes. 

The algorithm was applied to the MD simulations of a box of water molecules. The three-center water model was used [23]. The initial positions were at the equilibrium therefore all displacements were zero. The initial velocities were... 

In Table 1 the CPU time required by the two methods (LFV and SISM) for 1000 MD integration steps computed on an HP 735 workstation are compared for the same model system, a box of 50 water molecules, respectively. The computation cost per integration step is approximately the same for both methods so that th< syieed up of the SISM over the LFV algorithm is deter-... 

Fig. 2. The Macroscopic multipole algorithm creates exponentially larger aggregates of the original unit cell (small solid box in center) to rapidly build up a large but finite periodic system.

Pharma Algorithms, Toronto, Canada. Algorithm Builder VI.8 and ADME Boxes... 

G.C. and G.E. are indebted to the University of Turin for financial support. We also thank Pharma Algorithm (http //www.ap-algorithms.com) for the complimentary copy of the ADME Boxes software (version 3.5, release date November 2006). 

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