Fixes to example inputs in new documentation

src/generic/DumpAtoms.cpp

@@ -140,7 +140,7 @@ If the xdrfile library is installed properly the PLUMED configure script should
 detect it and enable it.  The following example shows how you can use DUMPATOMS to output an xtc file:
 
 ```plumed
-c1: COM ATOMS=11-20 LABEL=c1
+c1: COM ATOMS=11-20
 DUMPATOMS STRIDE=10 FILE=file.xtc ATOMS=1-10,c1
 ```
 

src/generic/GatherReplicas.cpp

@@ -48,7 +48,7 @@ d: DISTANCE ATOMS=1,2
 # Now gather the values of this distance on all the replicas:
 g: GATHER_REPLICAS ARG=d
 # Now average the two distances on the two replicas
-s: COMBINE ARG=g.rep-0,g.rep-1 COEFFICIENTS=0.5,0.5 PERIODIC=NO
+s: COMBINE ARG=g.rep-1,g.rep-2 COEFFICIENTS=0.5,0.5 PERIODIC=NO
 # And print the instaneous average for the distance on the two replicas
 PRINT ARG=s FILE=colvar
 ```
@@ -59,7 +59,7 @@ Now suppose that we wanted to calculate a time average of the distance and an av
 #SETTINGS NREPLICAS=2
 d: DISTANCE ATOMS=1,2
 g: GATHER_REPLICAS ARG=d
-s: COMBINE ARG=g.rep-0,g.rep-1 COEFFICIENTS=0.5,0.5 PERIODIC=NO
+s: COMBINE ARG=g.rep-1,g.rep-2 COEFFICIENTS=0.5,0.5 PERIODIC=NO
 # This does the time averaging
 a: AVERAGE ARG=s 
 # And output the final average

src/generic/PDB2Constant.cpp

@@ -123,11 +123,14 @@ You can read in these reference values by using the PDB2CONSTANT command as foll
 
 ```plumed
 #SETTINGS INPUTFILES=regtest/mapping/rt-pathtools-4/epath.pdb
+t1: TORSION ATOMS=1,2,3,4
+t2: TORSION ATOMS=5,6,7,8
 t1_ref: PDB2CONSTANT REFERENCE=regtest/mapping/rt-pathtools-4/epath.pdb ARG=t1
 t2_ref: PDB2CONSTANT REFERENCE=regtest/mapping/rt-pathtools-4/epath.pdb ARG=t2
 ``` 
 
-Notice that separate PDB2CONSTANT commands are required for reading in `t1` and `t2`.  Furthermore, because the 
+Notice that the input must define values with the labels that are being read in from the reference file
+and that separate PDB2CONSTANT commands are required for reading in `t1` and `t2`.  Furthermore, because the 
 input PDB file contains multiple frames vectors containing all the values for `t1` and `t2` are output from 
 the constant commands that are created by the shortcuts in the above input.  If you want to read only one of the 
 configurations in the input PDB file you can use a pdb with a single frame or the `NUMBER` keyword described above.

src/multicolvar/DumpMultiColvar.cpp

@@ -31,7 +31,7 @@ at the expanded version of the shortct in the example input below:
 
 ```plumed
 c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}
-DUMPMULTICOLVAR DATA=dd FILE=coords.xyz
+DUMPMULTICOLVAR DATA=c1 FILE=coords.xyz
 ```
 
 */