APBS 1.4.2.1 (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.

Notes

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.