Ladme/gorder: gorder v0.5.0

Version 0.5 of gorder: More features, more colors

Changes in version 0.5

• Dynamic membrane normal calculation: Membrane normals can be now calculated dynamically from actual membrane shape which allows the calculation of order parameters for vesicles and similar systems (see the manual).
• Ignoring PBC: You can now choose to ignore periodic boundary conditions. This allows analyzing simulations with non-orthogonal simulation boxes with some small additional friction (making molecules whole). See the manual for more information.
• Reworked manual lipid assignment: It is now possible to classify lipids into membrane leaflets using NDX files, enabling integration of gorder with FATSLiM. BREAKING CHANGE The keywords to request manual leaflet assignment using a leaflet assignment file have been changed, see the manual for more information.
• Ordermaps visualization: A python script is now generated inside any created ordermaps directory which can be used to easily plot the ordermaps. Changed the default range of the colorbar in ordermaps to more reasonable values.
• More trajectory formats: Added experimental support for more trajectory formats, namely TRR, GRO, PDB, Amber NetCDF, DCD, and LAMMPSTRJ. Always prefer using XTC trajectory as gorder is optimized to read it very fast. There are also some limitations connected with using different trajectory formats, see the manual.
• Bug fixes and other changes:
  • gorder now returns an error if the center of geometry calculation for leaflet classification is nonsensical (i.e., nan).
  • If molecule classification runs longer than expected, progress is logged. By default, progress output begins after 500 ms, but you can adjust this delay using the environment variable GORDER_MOLECULE_CLASSIFICATION_TIME_LIMIT.
  • Added more color to information written to standard output during analysis. Changed logging for output file writing. Changed logging for molecule types.
  • Reading an ndx file with invalid or duplicated group names no longer results in a hard error but instead raises a warning.