gromacs-5.1.0 beta patch

This reverts commit b148b715.

- 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

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

Same as 423d49bf applied to gmx 5.0

Needs gromacs to be repatched

Workaround for #132.

Notice that gromacs wants something like -0.5*f*x,
whereas plumed provides something like -f*x.

Additionally, for not so clear reasons, when using plumed without computing
ENERGY the virial contribution from plumed was completely ignored.

There are two workarounds in this patch:
1. In case plumed does not ask gromacs to compute ENERGY, the plumed contribution
   to virial is stored on a separate tensor and added to the gromacs one at the end
2. In case plumed asks gromacs to compute ENERGY, the a temporary tensor
   is created containing twice the gromacs virial and passed to plumed. The virial
   is then set to half of it.

This should solve both the issues discussed in #132

Needs gromacs to be repatched.

[makedoc]

Using numgroup as suggested by @swails on amber mailing list

(cherry picked from commit 200f4cb42744926a027e30393e56d315f24cd535)

Before this fix, amber was working correctly with multiple
replicas but not working correctly with a single replica.

Now both situations should be ok.

Notice that I used a hack to detect if replicas are present
or not in sander. Probably this should be cleaned up in
some way

(cherry picked from commit 0b7dc44635708e821e14ed6f1156317807e6db7d)

It should now work properly

(cherry picked from commit 6f96353a8a7975f7429426bce3777fb555deed65)

close #124

Since ambertools are released under the GPL 3 license, we can
store originals here. This is going to make future merges easier.

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

Closes #106

related to #113

Closes #113

(no real change, the relevant files where not modified in gmx)

it should works, but more tests are needed

Same as 55bc92d2
(written by Carlo), but in such a way that it results as a git mv

(will be reintroduced with next commit)

I added the possibility to pass kbT from gromacs to plumed.
To allow compatibility between old and new versions, I used the API
number. Namely: gromacs checks that plumed API>1; if so, pass the
temperature.

KbT is only used in METAD so far (not in HISTOGRAM)

Addresses #35

(cherry picked from commit e1d01e84)