removed condition that seemed to create very large support
in sum hills calculation and resulting into a very large computational
time. Credits to Carolyn Phillips from the mailing list.

gromacs-5.1.0 beta patch

[makedoc]

This reverts commit b148b715.

This should go with a94b94b2

[makedoc]

Similarly to what happens in Colvar class, I made
also for ActionWithVirtualAtom a method setBoxDerivativesNoPbc
that can be used to set the virial contribution when the Pbc have not
been used in the calculation of derivatives.

This should make the addition of new vatom actions easier

For DISTANCE, ANGLE, TORSION and PUCKERING,
I implemented something similar to GYR, where atoms coordinates
are first made whole, then the virial is computed assuming them whole.

Notice that modified coordinates are the local ones, so that the
change does not impact other actions.

Moreover, this required fixing numerical errors in a couple of regtests

Only add to the manual RESTART UPDATE_FROM and UPDATE_UNTIL
in the actions for which this makes sense

It seems the lapack routine I took from gromacs are not threadsafe.
Indeed, routines slasq5 and dlasq5 contained static variables.
I removed all of them and everything seems to still work correctly.
This seems to solve the problem that @gtribello
found in his no-buffer branch.

an INCLUDE, i cannot figure out if there was a reason for that

[makedoc]

Now all png needed for the manual are copied to html dir

[makedoc]

I put no box info in the first frame so as to check this:
f4ca4c5d.

There was an extra copy of the box in ActionAtomistic,
namely ActionAtomistic::box and ActionAtomistic::pbc.

This means that one should take care of both copies when changing it,
which is error prone.

I eliminated ActionAtomistic::box

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