APBS 0.2.3 (2002-10)ΒΆ

  • Fixed bugs in salt-dependent Helmholtz/nonlinear term of PBE affecting both LPBE and NPBE calculations. While this bug fix only changes most energies by < 2 kJ/mol, it is recommended that all users upgrade. Many thanks to Michael Grabe for finding and carefully documenting this bug!

  • A parameter (chgm) has been added which controls the charge discretization method used. Therefore, this version contains substantial changes in both the API and input file syntax. Specifically:

    • PBEparm has two new members (chgm, setchgm)
    • Vpmg_fillco requires another argument
    • Vpmg_*Force functions require additional arguments
    • Input files must now contain the keyword “chgm #” where # is an integer
    • Please see the documentation for more information.
  • Fixed problems with “slicing” off chunks of the mesh during I/O of focused calculations

  • Updated authors list

  • New CHARMM parameters – Robert Konecny

  • Created enumerations for common surface and charge discretization methods

  • Added Vmgrid class to support easy manipulation of nested grid data

  • Added more verbosity to error with NPBE forces

  • Added working Python wrappers – Todd Dolinksy

  • Modified VMD scripts read_dx and loadstuff.vmd