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.

Copy only necessary files

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(pointed out by Pratyush Tiwary)

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Now items are properly ordered in the pdf

I added some info about the automatic gzipping of directories.

Tutorial files are now stored as directories, making
merge easier.

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I made it such that if one put an "additional file"
that is actually a directory the directory is targzipped
when compiling the manual. This allows to keep in the git
repository real files (instead of tarballs) which are
then easier to merge.

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Now it sets the environment properly also in linux

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Conflicts:
	user-doc/figs/belfast-2-ala.png
	user-doc/figs/belfast-2-transition.png

(these figures were shrinked in both munster and cambridge branches)

This reverts commit d00cb5a0.

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1ns US
10ns metd

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