use recommended CHARMM NB values

See http://lists.gromacs.org/pipermail/gmx-users/2012-November/076091.html
MDP oplsaa changes

- increase Parrinello-Rahman time constant to 1.0 ps
- created GPU mdp file (with Verlet list and decreased energy and nstlist freq)
experimental CHARMM27 GPU mdp file (DO NOT USE)
fixed logging level: each command is logged again

Each command invocation is logged to the log file at level DEBUG (if the logger has been enabled, eg
with gromacs.start_logger()). This did not work for a while because the code for throttling looging
was buggy. With the help of http://stackoverflow.com/questions/6948190/python-logging-reverse-effects-of-disable
it seems to be working now.
gromacs.setup.solvate(): accept standard bt flag

Accept bt in preference to boxtype (avoids some very stupid setup problems when the user becomes confused
about usage that is close but not identical to editconf).
fixed: Manager config parser ignored floats
fixed error in gromacs.setup.solvate(): bt takes precedence over boxtype
gromacs.setup.solvate(): fixed none.mdp for Gromacs 4.6

grompp in 4.6 rejects a mdp file with rcoulom = rvdw = rlist = 0 so
I added bogus entries. Does not matter because the file is only needed
so that grompp calculates the total charge using the selected FF.
gromacs.setup.solvate(): default ion names are now NA and CL (as in OPLS-AA)
fixed: cbook.grompp_qtot() would miss non-zero charge

- In some revision of Gromacs, grompp started outputting the total charge
  on standard error but this function only filtered stdout. The result
  was that a total charge was erroneously reported as 0 even if it was
  non-zero.

  This has now been fixed by simply analysing ALL grompp output (i.e.
  both stdout and stderr).

- Furthermore, the regular expression was refined so that it captures
  both scientific notation and simple decimal notation.
setup.MD_restrained(): use refcoord_scaling = "com"

- grompp complains about position restraint runs and P-coupling
- _setup_MD(): moved cleaning up of returned kwargs into returning
  function for better control (eg MD_restrained() is removing the
  refcoord_scaling settings)
fixed Issue #11: gw-join_parts.py sets fulldir/partsdir correctly
adjustments for release 0.3.1

- set as release
- added rst suffixes to README and INSTALL so that github shows them
  formatted
- updated CHANGELOG from git log
doc updates

- put INSTALL and README under Installation
- removed edPDB from README (code had been removed a while back)
- changed doc layout to standard orange sphinx doc
- added logo
documentation for 0.3.1
bumped version to 0.3.2-devel
Fixed reST docs in gromacs and logger outputs release (version)
Simulation class: show ndx in status message
fixed Transformer.fit(): removed centering

The Transformer.fit() command (and also trj_xyfitted()) contained
trjconv options to center while fitting. This does not work well together
and really only rotations are properly removed. The fitting was removed
which improves the quality of the fitted trajectories substantially
(also for the StripWater plugin).
scripts/gw-fit_strip_trajectories.py: can use custom group for centering

A custom group for centering helps for e.g. dimers: choose a small
group at the dimer interface.