- updated patch to include api version
- updated patch to inclide virial fix
- updated patch to gromacs 4.5.7

hopefully will avoid some mail to the mailing list

I implemented a framework to provide the virial corrections for
virtual atoms that are non-linear functions

I added the possibility to dump the 9 components of the virial
from the driver.

This is not strictly necessary since virial is
set anyway (and not accumulated), but I added
it for consistency.

If you had your atoms distributed among the domains such that one
node had on all the Atoms there could be a problem in running plumed.
This change fixes this problem.  Also deleted rogue check in
AdjacencyMatrixAction

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I changed a few things:
1. instead of checking with "--enable-debug" and "--enable-debug --enable-debug-glibcxx"
  I always use both.
2. I check with debug flags and serial compiler (before it was only debug+MPI)
3. I changed the order so that runs with manual is the first and runs
  with debug options are also made earlier. This is convenient since they
  take more time

This allows reading crd files without linking external plugins

(goes with 32c10c65)

ReferenceConfiguration::getReferencePositions() was hidden by
ReferenceAtoms::getReferencePositions()
since the former was const. I changed the former to non const.

@gtribello might want to check this

Multiple processors per replica. Forces are also checked

A collective variable value was passed instead of its index.
Found thanks to bound checking!

@carlocamilloni you might want to double check

If they are not too slow, they could be useful for finding bugs

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Notice that these tests will not run on travis-ci
since VMD plugins are not available there

This allow amber formats to be properly read

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This bug was not detected since it only appears if the reference pdb
has center not in the origin. I also added an extra regtest to check for
this

I changed modifyForce to modifyGlobalForce. Notice that other modifyXX
methods in ActionAtomistic are returning the local copy. "Global"
makes more clear that one is modifying the global copy of forces.

I also added modifyGlobalVirial with an analogous functionality

Fixes a potential problem in the following commits:
423d49bf
bb6178a2
(reported by C. Perego)

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