APBS 1.1.0 (2009-03)

New features

  • Moved APBS user guide and tutorial to MediaWiki
  • Added in support for OpenMPI for parallel calculations
  • Added in command line support for Opal job submissions (Code by Samir Unni)
  • Allowed pathname containing spaces in input file, as long as the whole pathname is in quotes (“”)
  • Documented ‘make test’ and related features

Modifications

  • Modified the function bcCalc to march through the data array linearly when setting boundary conditions. This removes duplication of grid points on the edge of the array and corners.
  • Clarified documentation on the IDs assigned to input maps, PQRs, parameter files, etc.
  • pdated tutorial to warn against spaces in APBS working directory path in VMD; updated user guide to warn against spaces in APBS installation path on Windows
  • ‘make test’ has been reconfigured to run before issuing make install (can be run from top directory)
  • Removed tools/visualization/vmd from tools directory in lieu of built-in support in VMD
  • Path lengths can now be larger than 80 characters
  • Expanded authorship list
  • Added in ‘make test-opal’ as a post install test (run from the examples install directory)
  • Added additional concentrations to protein-rna test case to better encompass experimental conditions used by Garcia-Garcia and Draper; this improves agreement with the published data

Bug fixes

  • Fixed typos in User Guide (ion keyword) and clarified SMPBE keyword usage
  • Fixed typo in User Guide (writemat: poission -> poisson)
  • Updated psize.py with Robert’s patch to fix inconsistent assignment of fine grid numbers in some (very) rare cases
  • Fixed bug with boundary condition assignment. This could potentially affect all calculations; however, probably has limited impact: many test cases gave identical results after the bug fix; the largest change in value was < 0.07%.