CHANGES

==============================
 CHANGELOG for GromacsWrapper
==============================

2013-08-07     0.3.2  
orbeckst, andy.somogyi

* fixed setup.make_main_index() by using a workaround for a bug in make_ndx
  when multiple groups have the same name (use the first one)
* improvements in cbook.Transformer and the StripWater plugin (can
  write output to specified directory)
* gw-fit_strip_trajectories.py: can use a custom group for centering
  (necessary when dealing with multimeric proteins that might get
  split across the periodic boundaries)  


2012-12-10     0.3.1
orbeckst, jandom

* added IndexBuilder.write() method to safely write named index groups
* new HBonds hydrogen bonding analysis plugin (uses g_hbond and can
  return individual hbond existence probabilities)
* XVG has initial support to plot periodic data such as dihedral angles
* ITP reader: 
  - ITP.contains_preprocessor_constructs() to check if the
    itp file uses some of the recognized preprocessing directives
  - new set_data() method to completely rebuild a topology
* set environment variable GROMACSWRAPPER_SUPPRESS_SETUP_CHECK to true
  in order to avoid be notified of missing config files
* example scripts are installed (all example script names start
  with gw-*)
  - gw-fit_strip_trajectories.py: remove water and fit to protein
  - gw-join_parts.py: concatenate xtc, trr, edr, log for simulations
    done in parts (and with -noappend)
  - gw-merge_topologies.py: join multiple building block topologies 
* updated MDP templates
  - increase Parrinello-Rahman time constant to 1.0 ps
  - use refcoord_scaling = "com" for position restraints
  - use recommended CHARMM NB values
* fixed: cbook.grompp_qtot() would miss non-zero charge
* fixed: Manager config parser ignored floats
* gromacs.setup.solvate()
  - default ion names are now NA and CL
  - adapted for Gromacs 4.6
  - bt takes precedence over boxtype


2012-04-24     0.3.0   
orbeckst

* improved file format handling (ITP (incomplete, but uses a
  preprocessor), XPM, XVG (can do fairly fancy coarse-grained
  plotting and error analysis))
* output can be captured to a capture file (uses the new
  gromacs.environment framework)
* fixes for cbook.Transformer
* removed deprecated edPDB (use MDAnalysis instead)
* example script fit_strip_trajectory.py
* scipy is now a package dependency (use in numkit and then XVG)

Earlier releases did not have an explicit change log. See the commit
history at https://github.com/orbeckst/GromacsWrapper for details.