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DiTe2: Calculating the diffusion tensor for flexible molecules
Author(s) -
Campeggio Jonathan,
Polimeno Antonino,
Zerbetto Mirco
Publication year - 2019
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.25742
Subject(s) - dihedral angle , tensor (intrinsic definition) , diffusion , flexibility (engineering) , atom (system on chip) , molecule , physics , classical mechanics , statistical physics , computer science , geometry , mathematics , thermodynamics , quantum mechanics , hydrogen bond , statistics , embedded system
We report on an extended hydrodynamic modeling of the friction tensorial properties of flexible molecules including all types of natural, Z‐Matrix like, internal coordinates. We implement the new methodology by extending and updating the software DiTe [Barone et al. J. Comput. Chem. 30, 2 (2009)]. DiTe (DIffusion TEnsor) implements a hydrodynamic modeling of the generalized translational, rotational, and configurational friction and diffusion tensors of flexible molecules in which flexibility is described in terms of dihedral angles. The new tool, DiTe2, has been renewed to include also stretching and bending types of internal mobility. Furthermore, DiTe2 is able to calculate the friction and diffusion tensors along collective (or reaction) coordinates defined as linear combinations of the internal natural ones. A number of tests are reported to show the new features of DiTe2. As leitmotiv for the tests, the calmodulin protein is taken into consideration, described both at all‐atom and coarse‐grained levels. © 2018 Wiley Periodicals, Inc.