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Volumn 114, Issue 5, 2001, Pages 2079-2089

A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL GEOMETRY; COMPUTER SIMULATION; DEGREES OF FREEDOM (MECHANICS); FREE ENERGY; TREES (MATHEMATICS); VISUALIZATION;

EID: 0034825161     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1330216     Document Type: Article
Times cited : (25)

References (61)
  • 4
    • 0032415318 scopus 로고    scopus 로고
    • In systems composed of different chemical elements, separate distance matrices are required for each element
    • F. R. Manby, R. L. Johnston, and C. Roberts, MATCDY 38, 111 (1998). In systems composed of different chemical elements, separate distance matrices are required for each element.
    • (1998) MATCDY , vol.38 , pp. 111
    • Manby, F.R.1    Johnston, R.L.2    Roberts, C.3
  • 14
    • 33645739131 scopus 로고    scopus 로고
    • note
    • rs, as the dissimilarity between configurations r and s and n the number of configurations. The need for diagonalization of B makes metric multidimensional scaling impractical on more than a few thousand configurations on current computers. However, additional points can be embedded in that space, using only dissimilarities to the points previously embedded (Ref. 33). The nature of the embedding will depend on which points were used to span the space; in an iterative procedure, it is conceivable to use either a diverse subset of points, leading to similar distortions for all points, or to use a representa-live subset, reducing the distortion in those regions which are most heavily populated.
  • 25
    • 33645737457 scopus 로고    scopus 로고
    • note
    • A space with a number of embedded points can be decomposed into cells, the Voronoi polyhedra, each comprising one point such that the space enclosed by a cell is closer to the corresponding point than to any other. A Delaunay diagram is the dual of its Voronoi diagram (see any textbook on Computational Geometry): every two points whose' Voronoi polyhedra share a face become Delaunay neighbors. If the points are nondegenerate, their Delaunay graph is a triangulation. Delaunay triangulations are optimal in the sense of avoiding long, skinny triangles.
  • 35
    • 33645728416 scopus 로고    scopus 로고
    • J. J. Jensen, http://hendrix.imm.dtu.dk/software/.
    • Jensen, J.J.1
  • 39
    • 0001465710 scopus 로고
    • Computing in Euclidean Geometry, edited by D.-Z. Du and F. Hwang, World Scientific, Singapore
    • S. Fortune, In Computing in Euclidean Geometry, edited by D.-Z. Du and F. Hwang, Vol. 4 of Lecture notes series on Computing, 2nd ed. (World Scientific, Singapore, 1995), pp. 225-265.
    • (1995) Lecture Notes Series on Computing, 2nd Ed. , vol.4 , pp. 225-265
    • Fortune, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.