A central partition of molecular conformational space. IV: Extracting information from the graph of cells

DOI10.1007/S10910-008-9384-5MaRDI QIDQ552032zbMATH OpenOpenAlexFDO

Authors Jacques Gabarro-Arpa

Publication date 21 July 2011

Published in Journal of Mathematical Chemistry (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/physics/0611108

zbMATH Keywords

face latticehyperplane arrangementmolecular conformational spacemolecular dynamics

Mathematics Subject Classification ID

Partitions of sets (05A18) Molecular physics (81V55)

Abstract: In previous works [physics/0204035, physics/0404052, physics/0509126] a procedure was described for dividing the $3imesN$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data sampled in molecular dynamics trajectories: the graph of cells, that encodes the set of cells in conformational space that are visited by the system in its thermal wandering. Here we outline a set of procedures for extracting useful information from this structure: 1st) interesting regions in the volume occupied by the system in conformational space can be bounded by a polyhedral cone whose faces are determined empirically from a set of relations between the coordinates of the molecule, 2nd) it is also shown that this cone can be decomposed into a hierarchical set of smaller cones, 3rd) the set of cells in a cone can be encoded by a simple combinatorial sequence.

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Cites work

• A central partition of molecular conformational space. I: Basic structures
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Cited in

(2)

• A central partition of molecular conformational space. I: Basic structures
• A central partition of molecular conformational space. III. Combinatorial determination of the volume spanned by a molecular system

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