gromacs-5.1.0 beta patch

- restart

ActionWithVirtualAtoms should clean up the force on the virtual
atom when applied. Otherwise, actions computing the force on the
center of mass (such as FIT_TO_TEMPLATE) could compute it
wrongly when virtual atoms are defined.

I also modified a regtest so that it checks what happen when
using COM after FIT_TO_TEMPLATE

[makedoc]

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

Notice that this only works with APIversion>2, that is
with the to-be-released PLUMED 2.2

Added a new cmd "setRestart" that allow setting restart
from MD engine.

This setting can be overridden by PLUMED using:
RESTART
or
RESTART OFF
to respectively switch on or off restart from PLUMED input.

Notice that this would break compatibility in the sense that
it would turn on restart automatically without the user
specifying it.

I increased the APIversion to 3 so that MD engines can
check if PLUMED support this keyword before using it.

This fixes #100

Now file reader properly reads:
* dos and unix newlines ("\n" and "\r\n")
* files without end of line (emacs)

I didn't implement mac newlines ("\r") because it's more complicated
and I think nobody cares.

as an enviroment variable. This should allow to move
more easily a static executable of plumed.

I have implemented solutions 2 and 4 of #129

this close #129

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.