Chem-Bio Informatics Journal
Online ISSN : 1347-0442
Print ISSN : 1347-6297
ISSN-L : 1347-0442
Search
Advanced search
OR
Browse
Search
Volume 14
Displaying 1-2 of 2 articles from this issue
Show all abstracts
    • |<
    • <
    • 1
    • >
    • >|
Original
  • Fragment molecular orbital−based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion
    Yuji Kato, Takayuki Fujiwara, Yuto Komeiji, Tatsuya Nakano, Hirotoshi ...
    2014 Volume 14 Pages 1-13
    Published: July 04, 2014
    Released on J-STAGE: July 04, 2014
    DOIhttps://doi.org/10.1273/cbij.14.1
    JOURNAL FREE ACCESS
    Show abstractHide abstract
    A simulation protocol based on fragment molecular orbital−based molecular dynamics (FMO-MD) was applied to a droplet model consisting of a divalent copper ion and 64 water molecules. The total energy and forces were evaluated at the unrestricted Hartree-Fock (UHF) level with three-body fragment correction (FMO3). Two MD runs were performed: one with a six-coordination setting and the other with a five-coordination setting in the first hydration shell. Both runs resulted in the main peak position of the Cu-O radial distribution function at 2.02 Å, in reasonable agreement with the experimental data. The O-Cu-O angular distribution function showed different characteristics between the two cases.
    View full abstract
    Download PDF (507K)
  • Optimal damping algorithm for unrestricted Hartree-Fock calculations
    Jun-ichi Yamamoto, Yuji Mochizuki
    2014 Volume 14 Pages 14-33
    Published: September 12, 2014
    Released on J-STAGE: September 13, 2014
    DOIhttps://doi.org/10.1273/cbij.14.14
    JOURNAL FREE ACCESS
    Show abstractHide abstract
    We have developed a couple of optimal damping algorithms (ODAs) for unrestricted Hartree-Fock (UHF) calculations of open-shell molecular systems. A series of equations were derived for both concurrent and alternate constructions of α and β Fock matrices in the integral-direct self-consistent-field (SCF) procedure. Several test calculations were performed to check the convergence behaviors. It was shown that the concurrent algorithm provides better performance than does the alternate one.
    View full abstract
    Download PDF (517K)
    • |<
    • <
    • 1
    • >
    • >|
feedback
 Top