portability aspects in install guide + minor tweaks

Added information on portability aspects related to CPU instruction
sets, related to #1428.

Additionally, made several minor updates and tweaks related to
compilers, platforms, cmake, etc.

Change-Id: I621262c939c119e5bdd5e7c91dda0ae3ffc60b7b
Permit warning-free use of Andersen thermostat

Simulations using Andersen thermostat don't need to remove center of
mass motion, because that is intrinsic to the algorithm. Using it with
nstcomm > 1 generated a warning that center-of-mass removal is
unnecessary. Using it with nstcomm == 0 generated a warning that
ice-cube artifacts might be generated. Resolved by suppressing the
latter warning for both Andersen thermostats.

Change-Id: I6b2c1594cabd81964b3ba1ebc5dd61e0f1debb5e
Improved CUDA non-bonded kernel performance

Some old tweak which was supposed to improve performance had in fact
the opposite effect. Removing this tweak and with it eliminating 
shared memory bank conflicts it caused improved performance by up
to 2.5% in the force-only CUDA kernel.

Change-Id: I7fcb24defed2c68627457522c39805afc83b3276
Add fatal error for Andersen+constraints+DD

This combination produced a temperature that was 6.5 degrees higher
than the same with one domain, for a 1ns PME lysozyme in water
simulation.

Change-Id: I9f80276c47de955a5053bcabb6fe7c9bfdceaf0e
Fix incorrect grid cell size in g_sas -nopbc

Fixes #1445

Change-Id: I798fc8fe96608633f26d9a3500f83f39b44af008
Merge release-4-6 into master

Conflicts:
	admin/installguide/installguide.tex

3643d2a Add fatal error for Andersen+constraints+DD ignored
because already in master.

Change-Id: I6b3346503036e5b31bcc929daa5bcc9a04dde3bc
Merge "Merge release-4-6 into master"