Merge branch 'v2.0' into v2.0-hrex
Merge branch 'v2.0' into v2.0-hrex
Merge remote-tracking branch 'origin/v2.0' into v2.0-hrex
Patch for sander (AmberTools 14)

Tentative patch for sander.
It implements all features (including support for
MPI runs) except for replica exchange stuff.

Closes #106
Merge branch 'v2.0' into v2.0-hrex
Fixed derivatives in histogram

(backported from master, see commit 92717cb65fc1b2a67be0adb01c635c6fce0a905f)
Fixed regtest

After 4525d50f4babf4db72acf0831c49055558ebac66
changelog
Merge branch 'v2.0' into v2.1
Merge branch 'v2.1-sander' into v2.1
changelog
Amber can save originals

Since ambertools are released under the GPL 3 license, we can
store originals here. This is going to make future merges easier.
configure:
- added intel compilers to the list of standard compilers
- added a check that stops the configuration if --enable-almost is set but almost is not found
configure:
- if enable-gsl is used and gsl are not found stops with error
- give a warning if a default ON option cannot be activated
configure:
- it says if plumed will be compiled with MPI or not
wget should be already present on travis
Added -O3 and lapack to travis file
cleaner travis file

I removed all the commands to install latex.
Just as a secure copy, I leave the commands in .travis.install.doxygen
fix lapack for travis
Fixed phase in diagMatrix

Before this fix the phase was chosen enforcing the sum of the elements
of each eigenvector to be positive (see dd4bd09bf).
This does not work well when the
sum is numerically close to zero for some symmetry. With this fix I
set the first non-zero element of each eigenvector to be positive.
Hopefully it is more robust and make results better reproducible
for regtesting