DiTe2 : Calculating the diffusion tensor for flexible molecules
© 2018 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 40(2019), 4 vom: 05. Feb., Seite 697-705 |
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| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2019
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Brownian dynamics coarse graining diffusion tensor hydrodynamics reaction coordinates |
| Zusammenfassung: | © 2018 Wiley Periodicals, Inc. 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 |
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| Beschreibung: | Date Completed 16.03.2020 Date Revised 16.03.2020 published: Print-Electronic Citation Status PubMed-not-MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.25742 |