GridMAT-MD:Bug Fixes and Revisions

Here we will post a running list of bugs and their status, as well as improvements to the code and new features. Please check back occasionally to verify that you are using the most up-to-date version of GridMAT-MD. Also, let us know if there is a feature you would like to see implemented, or if you have added something new!

Version 2.0:
  • Bug fix: Cleaned up STDOUT. Fixed by WJA, 4/18/2013.
  • Bug fix: Several new and descriptive errors/warnings added. Fixed by WJA, 4/18/2013.
  • Bug fix: The CRYST1 record is now properly pulled from .pdb files. Fixed by WJA, 4/18/2013.
  • New feature: Multi-frame .pdb and .gro files can now be processed. Added by WJA, 4/18/2013.
  • New feature: An arbitrarily large number of lipids can be considered in each coordinate file. Added by WJA, 4/18/2013.
  • New feature: Three types of output file formats can be generated (column, vector, matrix). Added by WJA, 4/18/2013.
  • New feature: The output filename prefix is now customizable. Added by WJA, 4/18/2013.
  • Updated documentation: New information has been added, especially concerning file preparation and updated options in the parameter file. Added by WJA, 4/18/2013.
Version 1.0.3:
  • Bug fix: Incorrect handling of residue names in .pdb files. Fixed by WJA, 12/15/2009.
Version 1.0.2:
  • New feature: Output is now compatible with Gnuplot, via a post-processing script. Added by JAL, 6/29/2009.
  • Updated documentation: New information about how to use Gnuplot. Added by JAL, 6/29/2009.
Version 1.0.1:
  • New feature: Compatibility with .pdb files as input. Added by WJA, 1/15/2009.
  • Updated documentation: Additional information about output format and how to use Xmatrix. Added by JAL, 2/4/2009.
Version 1.0:
  • Bug fix: Incorrect thickness calculations in the absence of solvent. Fixed by WJA, 12/4/2008.

Upcoming versions:
  • Known bug: Residue names in .gro files longer than 4 characters are not processed correctly
    * This probably won't get fixed, since .gro format is fixed and proper renaming takes care of it.
  • New feature: Radial thickness plots
  • New feature: Compatibility with shuffled .gro files.
    * Since the introduction of Gromacs-4.0, shuffling has been eliminated. We may not end up adding this feature.

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