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