APBS (2016-01)

New features

  • Poisson-Boltzmann Semi-Anlytical Method (PB-SAM) packaged and built with APBS.
  • New Geometric flow API and improvements in speed.
  • Support for BinaryDX file format.
  • SOR solver added for mg-auto input file option.
  • DXMath improvements.
  • Test suit improvements: * APBS build in Travis-CI * Geometric Flow tests added. * Protein RNA tests enabled. * Intermediate results testing.
  • Example READMEs onverted to markdown and updated with latest results.

Bug fixes

  • OpenMPI (mg-para) functionality restored.
  • Fixed parsing PQR files that contained records other than ATOM and HETATM.
  • Geometric Flow boundary indexing bug fixed.
  • Build fixes: * Out of source CMake build are again working. * Python library may be built. * CentOS 5 binary builds for glibc compatibility. * Pull requests merged.
  • Removed irrelevant warning messages.


The following packages are treated as submodules in APBS: * Geometric Flow has been moved to its own repository. * FETk has been cloned so that we could effect updates. * PB-SAM lives here: https://github.com/Electrostatics/PB-SAM

Added a chat feature for users.

Known bugs

  • Travis CI Linux builds are breaking because Geometric Flow relies on C++11 and Travis boxen have an old GCC that does not support C++11. This also and issue for CentOS 5.
  • BEM is temporarily disabled due to build issues.
  • Geometric Flow build is currently broken on Windows using Visual Studio.