(cherry picked from commit 1045b03e40d5a7d85d98d5bcff2004cfbc9d7c81)

This reverts commit 7d1a173e.

This squeezes several commits. I leave a trace below

reverted useless changes
(cherry picked from commit 69a31941dd4af1e3faf47a86fe3a579b52e26f80)

Added tool to trim spaces on the left
(cherry picked from commit 1c00ccb0f4915dff597424538fc89c4f74aaaf63)

Improved space trimming in resname
(cherry picked from commit 569bd8b75a96897972c729b2d41e8130f837a009)

Improved molclass parser

Now fails when using wrong names such as "phixx-1" instead of "phi-1"
(cherry picked from commit 7a54dfbfbe466fef02c52bf4c0b8abacf7178b4d)

Small cleanup
(cherry picked from commit f106a4fc209edb605f16736b37eefb1dd3e9cd21)

(cherry picked from commit 0037c97559b3e86d5cfbd062ddc420654e6d9575)

(cherry picked from commit 3d165c2ec8dd2e21f55ea1d2d6d94e2e4c9c6b67)

(cherry picked from commit ac88fd3ce3e8ff55e69f7bac94cf3e46fdebcc03)

in MOLINFO added 2 new MOLTYPE for nucleic acids: “rna” and “dna”
components are: “@epsion-#”, “@gamma-#“, “@beta-#“, “@alpha-#“,
“@zeta-#“, “@chi-#”, “@v{0..4}-#“, “@base-#”, “@sugar-“ and “@back-#”

in PUCKERING the components are: “.phs”, “.amp”,“.Zx”,”.Zy”
derivatives are calculate only for “.Zx” and “.Zy”
(cherry picked from commit 58bf3be6341db37ab032c58e2767c55848a75492)

Conflicts:
	user-doc/bibliography.bib

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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

This reverts commit b46d0793.

This commit break several regtests. Most of the problems are harmless
numerical derivatives. However, the regtests on pbc hangs forever.
I have to further inspect this.

Taken from the fccubic branch of @ceriottm

The "while" implementation for orthorombic cells is slighlty faster,
so I decided to enable it by default.

The "while" implementation for Tools::pbc is either slower
or equivalent, so I did not include it.

I think the reason is that in the first case one can avoid a couple
of multiplications, whereas in the second this is more difficult
since images are implemented in scaled coordinates and require
anyway two matrix*vector multiplications.

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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)

The new multicolvar measures the inplanedistance i.e. the
distane from a plane defined by a vector connecting two atoms.
The new refernce distance measures the dot product distance
between two points

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It does not shift anymore the atoms to their original positions.

Notice that this makes its behavior consistent with WHOLEMOLECULES
where atoms are not restored in the backward loop.

This implies that (consistently) one cannot rely that shared atoms
(those accessed with modifyAtoms()) are in their original position
in the ::apply() methods.

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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