Gromacswrapper

whitead, dotsdl, orbeckst

* fixed: check_mdrun_success() works now for Gromacs 4 and Gromacs 5
(issue 64)
* fixed: MDRunner working for Gromacs 4 and Gromacs 5 (issue 64)
* fixed setup.energy_minimize() not falling back to single precision
mdrun (issue 63)
* fixed: added missing alias "gmx solvate" <--> "genbox" (issue 62)
* added keyword argument use_shell=True to Command() to make Popen use
the shell
* added template for Gromacs 4.6.x gromacswrapper.cfg
* improved testing

quantifiedcode-bot, orbeckst, jandom, whitead

* requires Python 2.7
* new: gromacs pre-processed topology reader
* Added backwards compatibility for scripts written using Gromacs 4.x syntax with Gromacs 5.x.
Tool calls prefixed with 'G_' will still work. (PR 46, Issue 26)
* removed gridmatmd plugin and GridMAT-MD.pl script (41), fixes
installation issues (40)
* Allows custom prefixes like gmx_mpi:mdrun and gmx:trjconv (48)
* Made it so GromacsWrapper can be imported and tools loaded even if they can't
be executed at import time.

orbeckst, richardjgowers

* primitive support for Gromacs 5.x
* fixed: gromacs.fileformats was not imported properly (PR 21)
* docs at http://gromacswrapper.readthedocs.org

orbeckst, jandom

* improvements to the xpm reader
* improvements to stripwater plugin and transformer
* additional logging of filenames in setup._MD()
* new repository URL: https://github.com/Becksteinlab/GromacsWrapper

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)

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