From: Nathan A. Baker <baker@ch...> - 2002-10-09 15:48:38
Version 0.2.3 of the APBS software is now available. Among other
changes and improvements, this version fixes a bug in the
Poisson-Boltzmann equation formulation which was introduced in version
0.2.0. For the test cases examined, this bug does not dramatically
affect the energies (usually less than 2 kJ/mol), however, it is
recommended that all users upgrade to the latest version.
There has also been a change in the input file syntax; a new "chgm"
keyword has been added which allows users to choose the charge
discretization method. Please see the documentation for more
The complete list of changes includes:
* 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.
- 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
Please see the documentation for more information.
* Fixed problems with "slicing" off chunks of the mesh during I/O of
* Updated authors list
* New CHARMM parameters -- Robert Konecny
* Created enumerations for common surface and charge discretization
* Added Vmgrid class to support easy manipulation of nested grid
* Added more verbosity to error with NPBE forces
* Added working Python wrappers -- Todd Dolinksy
* Modified VMD scripts read_dx and loadstuff.vmd
Thank you for your continuing interest in APBS.
-- Nathan Baker
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone: (314) 362-2040, Fax: (314) 362-0234
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