diff --git a/CHANGES/v2.3.txt b/CHANGES/v2.3.txt
index 77c17300863b3f60d8cef7425ca6b929c238c347..d985a7c18c9f00e804f3ba7835aa87dc79471ede 100644
--- a/CHANGES/v2.3.txt
+++ b/CHANGES/v2.3.txt
@@ -124,5 +124,6 @@ Fixes since 2.3b. Relevant things could be merged in the changelog above when we
 - (for developers) Active modules to enable regtests are chosen using `plumed config`.
 - New CV: \ref JCOUPLING
 - \ref PUCKERING now supports 6 membered rings.
+- Tutorials have been (partially) updated to reflect some of the changes in the syntax
 
 */
diff --git a/src/function/LocalEnsemble.cpp b/src/function/LocalEnsemble.cpp
index 5b32f2eed89149fb900b41d0bda9c563c27f4bca..aee9a076fabf3d24262de60d71aa1ee457500941 100644
--- a/src/function/LocalEnsemble.cpp
+++ b/src/function/LocalEnsemble.cpp
@@ -30,23 +30,45 @@ namespace function{
 
 //+PLUMEDOC FUNCTION LOCALENSEMBLE
 /*
-Calculates the replica averaging of a collective variable over multiple replicas.
+Calculates the average over multiple arguments.
 
-Each collective variable is averaged separately and stored in a component labelled <em>label</em>.cvlabel.  
-
-Note that in case of variables such as \ref CS2BACKBONE, \ref CH3SHIFTS, \ref NOE and \ref RDC it is possible
-to perform the replica-averaging inside the variable, in fact in those cases are the single experimental
-values that averaged before calculating the collective variable.
+If more than one collective variable is given for each argument then they
+are averaged separately. The average is stored in a component labelled <em>label</em>.cvlabel.  
 
 \par Examples
-The following input tells plumed to calculate the distance between atoms 3 and 5
-and the average it over the available replicas.
+The following input tells plumed to calculate the chemical shifts for four
+different proteins in the same simulation box then average them, calcualated
+the sum of the squared deviation with respect to the experiemntal values and
+applies a linear restraint.
 \verbatim
-dist: DISTANCE ATOMS=3,5 
-ens: ENSEMBLE ARG=dist
-PRINT ARG=dist,ens.dist
+MOLINFO STRUCTURE=data/template.pdb
+
+chaina: GROUP ATOMS=1-1640
+chainb: GROUP ATOMS=1641-3280
+chainc: GROUP ATOMS=3281-4920
+chaind: GROUP ATOMS=4921-6560
+
+WHOLEMOLECULES ENTITY0=chaina ENTITY1=chainb ENTITY2=chainc ENTITY3=chaind
+
+csa: CS2BACKBONE ATOMS=chaina NRES=100 DATA=data/ TEMPLATE=chaina.pdb NOPBC
+csb: CS2BACKBONE ATOMS=chainb NRES=100 DATA=data/ TEMPLATE=chainb.pdb NOPBC
+csc: CS2BACKBONE ATOMS=chainc NRES=100 DATA=data/ TEMPLATE=chainc.pdb NOPBC
+csd: CS2BACKBONE ATOMS=chaind NRES=100 DATA=data/ TEMPLATE=chaind.pdb NOPBC
+
+ensca: LOCALENSEMBLE NUM=4 ARG1=(csa\.ca_.*) ARG2=(csb\.ca_.*) ARG3=(csc\.ca_.*) ARG4=(csd\.ca_.*)
+enscb: LOCALENSEMBLE NUM=4 ARG1=(csa\.cb_.*) ARG2=(csb\.cb_.*) ARG3=(csc\.cb_.*) ARG4=(csd\.cb_.*)
+ensco: LOCALENSEMBLE NUM=4 ARG1=(csa\.co_.*) ARG2=(csb\.co_.*) ARG3=(csc\.co_.*) ARG4=(csd\.co_.*)
+enshn: LOCALENSEMBLE NUM=4 ARG1=(csa\.hn_.*) ARG2=(csb\.hn_.*) ARG3=(csc\.hn_.*) ARG4=(csd\.hn_.*)
+ensnh: LOCALENSEMBLE NUM=4 ARG1=(csa\.nh_.*) ARG2=(csb\.nh_.*) ARG3=(csc\.nh_.*) ARG4=(csd\.nh_.*)
+
+stca: STATS ARG=(ensca\.csa\.ca_.*) PARARG=(csa\.expca_.*) SQDEVSUM
+stcb: STATS ARG=(enscb\.csa\.cb_.*) PARARG=(csa\.expcb_.*) SQDEVSUM
+stco: STATS ARG=(ensco\.csa\.co_.*) PARARG=(csa\.expco_.*) SQDEVSUM
+sthn: STATS ARG=(enshn\.csa\.hn_.*) PARARG=(csa\.exphn_.*) SQDEVSUM
+stnh: STATS ARG=(ensnh\.csa\.nh_.*) PARARG=(csa\.expnh_.*) SQDEVSUM
+
+res: RESTRAINT ARG=stca.*,stcb.*,stco.*,sthn.*,stnh.* AT=0.,0.,0.,0.,0. KAPPA=0.,0.,0.,0.,0 SLOPE=16.,16.,12.,24.,0.5
 \endverbatim
-(See also \ref PRINT and \ref DISTANCE).
 
 */
 //+ENDPLUMEDOC
diff --git a/user-doc/tutorials/belfast-1.txt b/user-doc/tutorials/belfast-1.txt
index 3ce4f508a7bcfe0c4068cfccde9bf9b69d3ccfed..d08bccac7dceaf7974a1b3322e3766c7c1bedace 100644
--- a/user-doc/tutorials/belfast-1.txt
+++ b/user-doc/tutorials/belfast-1.txt
@@ -102,14 +102,14 @@ here I can write what I want it won't be read.
 
 Try to run it.
 
-Sometimes, when calculating a collective variable, you may not want to use the positions of a number of atoms directly. Instead you may wish to use the position of a virtual atom whose position is generated based on the positions of a collection of other atoms. For example you might want to use the center of mass of a group of atoms (\ref COM):
+Sometimes, when calculating a collective variable, you may not want to use the positions of a number of atoms directly. Instead you may wish to use the position of a virtual atom whose position is generated based on the positions of a collection of other atoms. For example you might want to use the center of a group of atoms (\ref CENTER):
 
 Since PLUMED executes the input in order you need to define the new Virtual Atom before using it:
 
 \verbatim
 
-first: COM ATOMS=1,2,3,4,5,6
-last: COM ATOMS=251-256
+first: CENTER ATOMS=1,2,3,4,5,6
+last: CENTER ATOMS=251-256
 
 e2edist: DISTANCE ATOMS=2,253
 comdist: DISTANCE ATOMS=first,last
@@ -119,17 +119,17 @@ PRINT ARG=e2edist,comdist STRIDE=1 FILE=COLVAR
 ENDPLUMED
 \endverbatim
 
-NOTE: an action (i.e. COM or DISTANCE here) can be either label using LABEL as we did before or as label: ACTION as we have just done here.
+NOTE: an action (i.e. CENTER or DISTANCE here) can be either label using LABEL as we did before or as label: ACTION as we have just done here.
 
 With the above input this is what happen inside PLUMED with a STRIDE=1:
 
-1. calculates the position of the Virtual Atom 'first' as the \ref COM of atoms from 1 to 6;
-2. calculates the position of the Virtual Atom 'last' as the \ref COM of atoms from 251 to 256;
+1. calculates the position of the Virtual Atom 'first' as the \ref CENTER of atoms from 1 to 6;
+2. calculates the position of the Virtual Atom 'last' as the \ref CENTER of atoms from 251 to 256;
 3. calculates the distance between atoms 2 and 253 and saves it in 'e2edist';
 4. calculates the distance between the two atoms 'first' and 'last' and saves it in 'comdist';
 5. print the content of 'e2edist' and 'comdist' in the file COLVAR
 
-In the above input we have used to different ways of writing the atoms used in \ref COM calculation:
+In the above input we have used to different ways of writing the atoms used in \ref CENTER calculation:
 
 1. ATOMS=1,2,3,4,5,6 is the explicit list of the atoms we need
 2. ATOMS=251-256 is the range of atoms needed
@@ -156,8 +156,8 @@ Virtual atoms can be used in place of standard atoms everywhere an atom can be g
 with standard atoms. So for example we can analyse the \ref TORSION angle for a set of Virtual and Standard atoms:
 
 \verbatim
-first: COM ATOMS=1-6
-last: COM ATOMS=251-256
+first: CENTER ATOMS=1-6
+last: CENTER ATOMS=251-256
 cvtor: TORSION ATOMS=first,102,138,last
 
 PRINT ARG=cvtor STRIDE=1 FILE=COLVAR 
@@ -261,14 +261,16 @@ PRINT ARG=abeta.lessthan,dd.mean,dd.min,dd.max,dd.moment-2 STRIDE=1 FILE=COLVAR
 
 HISTOGRAM ...
 ARG=abeta.lessthan,dd.mean
+LABEL=hh
 USE_ALL_DATA
-KERNEL=discrete
+KERNEL=DISCRETE
 GRID_MIN=0,0.8
 GRID_MAX=4,1.2
 GRID_BIN=40,40
-GRID_WFILE=histo
 ... HISTOGRAM
 
+DUMPGRID GRID=hh FILE=histo
+
 ENDPLUMED
 \endverbatim
 
@@ -286,15 +288,17 @@ and the BANDWIDTH should be smaller (i.e. one order of magnitude) than the varia
 
 \verbatim
 HISTOGRAM ...
+LABEL=hh
 ARG=abeta.lessthan,dd.mean
 USE_ALL_DATA
 GRID_MIN=0,0.8
 GRID_MAX=4,1.2
 GRID_SPACING=0.04,0.004
 BANDWIDTH=0.08,0.008
-GRID_WFILE=histo
 ... HISTOGRAM
 
+DUMPGRID GRID=hh FILE=histo
+
 ENDPLUMED
 \endverbatim
 
diff --git a/user-doc/tutorials/belfast-4.txt b/user-doc/tutorials/belfast-4.txt
index 44509bfc9bc3b77831725ef5e3e599c032a0397b..3531956e6a18c6cc342554fcef3f1f07ae31f907 100644
--- a/user-doc/tutorials/belfast-4.txt
+++ b/user-doc/tutorials/belfast-4.txt
@@ -209,7 +209,7 @@ The <a href="tutorial-resources/belfast-4.tar.gz" download="belfast-4.tar.gz">ta
 By working in the directory where the topol.tpr file is stored, one can launch gromacs
 with the command
 \verbatim
-mdrun_mpi -plumed plumed.dat -nsteps 100000
+gmx_mpi mdrun -plumed plumed.dat -nsteps 100000
 \endverbatim
 (notice that the -nsteps flag allows the number of steps to be changed).
 
@@ -409,7 +409,7 @@ restraint-phi: RESTRAINT ARG=phi KAPPA=40.0 AT=$AT
 PRINT STRIDE=10 ARG=phi,psi,restraint-phi.bias FILE=COLVAR$AT
 EOF
 
-mdrun_mpi -plumed plumed.dat -nsteps 100000 -x traj$AT.xtc
+gmx_mpi mdrun -plumed plumed.dat -nsteps 100000 -x traj$AT.xtc
 
 done
 
@@ -425,7 +425,7 @@ can be mixed and it is not necessary to keep track of which restraint was used t
 every single frame. Let's get the concatenated trajectory
 
 \verbatim
-trjcat -cat -f traj*.xtc -o alltraj.xtc
+gmx_mpi trjcat -cat -f traj*.xtc -o alltraj.xtc
 \endverbatim
 
 Now we should compute the value of each of the bias potentials on the entire (concatenated) trajectory
diff --git a/user-doc/tutorials/belfast-6.txt b/user-doc/tutorials/belfast-6.txt
index 4ab89bab7ad1bf4a42a0457020184628061a3bfb..edfdffc83b7c222d2f839eaf16d833c5f4f09c37 100644
--- a/user-doc/tutorials/belfast-6.txt
+++ b/user-doc/tutorials/belfast-6.txt
@@ -135,7 +135,7 @@ Once the PLUMED input file is prepared, one has to run Gromacs with the option t
 read the input file:
 
 \verbatim
-mdrun_mpi -plumed
+gmx_mpi mdrun -plumed
 \endverbatim
 
 During the metadynamics simulation, PLUMED will create two files, named COLVAR and HILLS.
diff --git a/user-doc/tutorials/belfast-7.txt b/user-doc/tutorials/belfast-7.txt
index 187aa2268d3e43c0dbc34149cab7717e56b06156..b81abd651fd9751472c1e852a54e96533b9542c3 100644
--- a/user-doc/tutorials/belfast-7.txt
+++ b/user-doc/tutorials/belfast-7.txt
@@ -119,7 +119,7 @@ PRINT STRIDE=10 ARG=phi,psi FILE=COLVAR
 To submit this simulation with Gromacs, we need the following command line.
 
 \verbatim
-mpirun -np 2 mdrun_mpi -s TOPO/topol -plumed -multi 2 -replex 100
+mpirun -np 2 gmx_mpi mdrun -s TOPO/topol -plumed -multi 2 -replex 100
 \endverbatim
 
 This command will execute two MPI processess in parallel, using the topology files
@@ -177,7 +177,7 @@ so there seems not to be any problem on this side.
 We can use the second file to reconstruct the continuous trajectories of each replica in temperature:
 
 \verbatim
-trjcat_mpi -f traj0.trr traj1.trr -demux replica_index.xvg
+gmx_mpi trjcat -f traj0.trr traj1.trr -demux replica_index.xvg
 \endverbatim
 
 and the following PLUMED input file (plumed_demux.dat) to recalculate the value of the CVs on the demuxed trajectories,
@@ -198,11 +198,11 @@ For the analysis of the demuxed trajectories, we can use the -rerun option of Gr
 
 \verbatim
 # rerun Gromacs on replica 0 trajectory
-mdrun_mpi -s TOPO/topol0.tpr -plumed plumed_demux.dat -rerun 0_trajout.xtc
+gmx_mpi mdrun -s TOPO/topol0.tpr -plumed plumed_demux.dat -rerun 0_trajout.xtc
 # rename the output
 mv COLVAR_DEMUX COLVAR_DEMUX.0
 # rerun Gromacs on replica 1 trajectory
-mdrun_mpi -s TOPO/topol1.tpr -plumed plumed_demux.dat -rerun 1_trajout.xtc
+gmx_mpi mdrun -s TOPO/topol1.tpr -plumed plumed_demux.dat -rerun 1_trajout.xtc
 # rename the output
 mv COLVAR_DEMUX COLVAR_DEMUX.1
 \endverbatim
@@ -236,7 +236,7 @@ of the simulation. We will now use 4 replicas at the following temperatures: 300
 We can use the same PLUMED input file described above (plumed.dat), and execute Gromacs using the following command line:
 
 \verbatim
- mpirun -np 4 mdrun_mpi -s TOPO/topol -plumed -multi 4 -replex 100
+ mpirun -np 4 gmx_mpi mdrun -s TOPO/topol -plumed -multi 4 -replex 100
 \endverbatim
 
 At the end of the simulation, we first monitor the diffusion in temperature space of each replica.
@@ -320,7 +320,7 @@ PRINT STRIDE=10 ARG=phi,psi,metad.bias FILE=COLVAR
 The PTMetaD simulation is executed in the same way as the PT:
 
 \verbatim
- mpirun -np 4 mdrun_mpi -s TOPO/topol -plumed -multi 4 -replex 100
+ mpirun -np 4 gmx_mpi mdrun -s TOPO/topol -plumed -multi 4 -replex 100
 \endverbatim
 
 and it will produce one COLVAR and HILLS file per temperature (COLVAR.0, HILLS.0, ...).
@@ -376,7 +376,7 @@ PRINT STRIDE=10 ARG=phi,psi,ene FILE=COLVAR_PT
 As usual, the simulation is run for 400ps using the following command:
 
 \verbatim
- mpirun -np 4 mdrun_mpi -s TOPO/topol -plumed plumed_PT.dat -multi 4 -replex 100
+ mpirun -np 4 gmx_mpi mdrun -s TOPO/topol -plumed plumed_PT.dat -multi 4 -replex 100
 \endverbatim
 
 At the end of the run, we want to analyze the acceptance rate between exchanges.
@@ -433,7 +433,7 @@ potential energy at 300K, as calculated from the preliminary PT run.
 We run the simulation following the usual procedure:
 
 \verbatim
- mpirun -np 4 mdrun_mpi -s TOPO/topol -plumed plumed_PTWTE.dat -multi 4 -replex 100
+ mpirun -np 4 gmx_mpi mdrun -s TOPO/topol -plumed plumed_PTWTE.dat -multi 4 -replex 100
 \endverbatim
 
 If we analyze the average acceptance probability in this run:
@@ -512,7 +512,7 @@ parameters and biasfactors in the two metadynamics runs.
 The simulation is carried out using the usual procedure:
 
 \verbatim
- mpirun -np 4 mdrun_mpi -s TOPO/topol -plumed plumed_PTMetaDWTE.dat -multi 4 -replex 100
+ mpirun -np 4 gmx_mpi mdrun -s TOPO/topol -plumed plumed_PTMetaDWTE.dat -multi 4 -replex 100
 \endverbatim
 
 
diff --git a/user-doc/tutorials/belfast-7/Exercise_3/plumed.dat.0 b/user-doc/tutorials/belfast-7/Exercise_3/plumed.0.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_3/plumed.dat.0
rename to user-doc/tutorials/belfast-7/Exercise_3/plumed.0.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_3/plumed.dat.1 b/user-doc/tutorials/belfast-7/Exercise_3/plumed.1.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_3/plumed.dat.1
rename to user-doc/tutorials/belfast-7/Exercise_3/plumed.1.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_3/plumed.dat.2 b/user-doc/tutorials/belfast-7/Exercise_3/plumed.2.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_3/plumed.dat.2
rename to user-doc/tutorials/belfast-7/Exercise_3/plumed.2.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_3/plumed.dat.3 b/user-doc/tutorials/belfast-7/Exercise_3/plumed.3.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_3/plumed.dat.3
rename to user-doc/tutorials/belfast-7/Exercise_3/plumed.3.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.dat.0 b/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.0.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.dat.0
rename to user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.0.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.dat.1 b/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.1.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.dat.1
rename to user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.1.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.dat.2 b/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.2.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.dat.2
rename to user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.2.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.dat.3 b/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.3.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.dat.3
rename to user-doc/tutorials/belfast-7/Exercise_4/plumed_PTMetaDWTE.3.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.dat.0 b/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.0.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.dat.0
rename to user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.0.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.dat.1 b/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.1.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.dat.1
rename to user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.1.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.dat.2 b/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.2.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.dat.2
rename to user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.2.dat
diff --git a/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.dat.3 b/user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.3.dat
similarity index 100%
rename from user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.dat.3
rename to user-doc/tutorials/belfast-7/Exercise_4/plumed_PTWTE.3.dat
diff --git a/user-doc/tutorials/belfast-8.txt b/user-doc/tutorials/belfast-8.txt
index 4f8e77c1bc96e1b38cbe3d717800dbddb5e1f00c..42ec571307dac69bd4323b1eb59fbc9add63e193 100644
--- a/user-doc/tutorials/belfast-8.txt
+++ b/user-doc/tutorials/belfast-8.txt
@@ -85,7 +85,7 @@ available).
 
 \verbatim
 INCLUDE FILE=plumed-common.dat
-be: METAD ARG=cv1 HEIGHT=0.2 SIGMA=0.2 PACE=100 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=200 
+be: METAD ARG=cv1 HEIGHT=0.2 SIGMA=0.2 PACE=100 GRID_MIN=-pi GRID_MAX=pi 
 PRINT ARG=cv1,cv2,cv3,cv4 STRIDE=1000 FILE=COLVAR
 \endverbatim
 
@@ -102,7 +102,7 @@ The four replicas start from the same GROMACS topology file replicated four time
 Finally, GROMACS is launched as a parallel run on 4 cores, with one replica per core, with the command 
 
 \verbatim
-mpirun -np 4 mdrun_mpi -s topol -plumed plumed -multi 4 -replex 2000 >& log &
+mpirun -np 4 gmx_mpi mdrun -s topol -plumed plumed -multi 4 -replex 2000 >& log &
 \endverbatim
 
 where -replex 2000 indicates that every 2000 molecular-dynamics steps
@@ -292,7 +292,7 @@ We can use the same common input file defined above and then we can define four
 was done above for bias-exchange but now all the biases are defined on the same collective variables:
 
 \verbatim
-plumed.dat.#
+plumed.#.dat
 INCLUDE FILE=plumed-common.dat
 
 METAD ...
@@ -302,10 +302,8 @@ SIGMA=0.3,0.3
 HEIGHT=0.2 
 PACE=100
 BIASFACTOR=8
-TEMP=300 
 GRID_MIN=-pi,-pi 
 GRID_MAX=pi,pi 
-GRID_BIN=200,200
 WALKERS_MPI
 ... METAD
 
@@ -315,7 +313,7 @@ PRINT ARG=cv1,cv2,cv3,cv4 STRIDE=1000 FILE=COLVAR
 and the simulation can be run in a similar way without doing exchanges:
 
 \verbatim
-mpirun -np 4 mdrun_mpi -s topol -plumed plumed -multi 4  >& log &
+mpirun -np 4 gmx_mpi mdrun -s topol -plumed plumed -multi 4  >& log &
 \endverbatim
 
 alternatively Multiple Walkers can be run as independent simulations sharing via the file system the biasing potential,
diff --git a/user-doc/tutorials/belfast-8/second/plumed.dat.0 b/user-doc/tutorials/belfast-8/second/plumed.0.dat
similarity index 76%
rename from user-doc/tutorials/belfast-8/second/plumed.dat.0
rename to user-doc/tutorials/belfast-8/second/plumed.0.dat
index d8458e50b55dc779eb7446260aaf10b23b557148..6d544022bfa9c795273850b009627fe71173aef5 100644
--- a/user-doc/tutorials/belfast-8/second/plumed.dat.0
+++ b/user-doc/tutorials/belfast-8/second/plumed.0.dat
@@ -1,3 +1,3 @@
 INCLUDE FILE=plumed-common.dat
-be: METAD ARG=cv1 HEIGHT=0.5 SIGMA=0.3 PACE=500 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=200 BIASFACTOR=10 TEMP=300
+be: METAD ARG=cv1 HEIGHT=0.5 SIGMA=0.3 PACE=500 GRID_MIN=-pi GRID_MAX=pi BIASFACTOR=10
 PRINT ARG=cv1,cv2,cv3,cv4 STRIDE=1000 FILE=COLVAR
diff --git a/user-doc/tutorials/belfast-8/second/plumed.dat.1 b/user-doc/tutorials/belfast-8/second/plumed.1.dat
similarity index 76%
rename from user-doc/tutorials/belfast-8/second/plumed.dat.1
rename to user-doc/tutorials/belfast-8/second/plumed.1.dat
index 05c7e75d54c9757bd534b88987c680733c37bf12..9ea9868fa3374a3080047d5be3b457b61eadee0d 100644
--- a/user-doc/tutorials/belfast-8/second/plumed.dat.1
+++ b/user-doc/tutorials/belfast-8/second/plumed.1.dat
@@ -1,4 +1,4 @@
 INCLUDE FILE=plumed-common.dat
-be: METAD ARG=cv2 HEIGHT=0.5 SIGMA=0.3 PACE=500 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=200 BIASFACTOR=10 TEMP=300
+be: METAD ARG=cv2 HEIGHT=0.5 SIGMA=0.3 PACE=500 GRID_MIN=-pi GRID_MAX=pi BIASFACTOR=10
 PRINT ARG=cv1,cv2,cv3,cv4 STRIDE=1000 FILE=COLVAR
 
diff --git a/user-doc/tutorials/belfast-8/second/plumed.dat.2 b/user-doc/tutorials/belfast-8/second/plumed.2.dat
similarity index 76%
rename from user-doc/tutorials/belfast-8/second/plumed.dat.2
rename to user-doc/tutorials/belfast-8/second/plumed.2.dat
index 7e6a89de0a0227b3d3d2ccb6e980c535cf22ea28..6b33d2f50cd29c9d16c7b6cafade1cd3c3560a55 100644
--- a/user-doc/tutorials/belfast-8/second/plumed.dat.2
+++ b/user-doc/tutorials/belfast-8/second/plumed.2.dat
@@ -1,3 +1,3 @@
 INCLUDE FILE=plumed-common.dat
-be: METAD ARG=cv3 HEIGHT=0.5 SIGMA=0.3 PACE=500 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=200 BIASFACTOR=10 TEMP=300
+be: METAD ARG=cv3 HEIGHT=0.5 SIGMA=0.3 PACE=500 GRID_MIN=-pi GRID_MAX=pi BIASFACTOR=10
 PRINT ARG=cv1,cv2,cv3,cv4 STRIDE=1000 FILE=COLVAR
diff --git a/user-doc/tutorials/belfast-8/second/plumed.dat.3 b/user-doc/tutorials/belfast-8/second/plumed.3.dat
similarity index 76%
rename from user-doc/tutorials/belfast-8/second/plumed.dat.3
rename to user-doc/tutorials/belfast-8/second/plumed.3.dat
index 217be74c7501b2660d0f055dca18444ab7baedc4..aca16a2905b64203d464bb0914c1cc354e572489 100644
--- a/user-doc/tutorials/belfast-8/second/plumed.dat.3
+++ b/user-doc/tutorials/belfast-8/second/plumed.3.dat
@@ -1,3 +1,3 @@
 INCLUDE FILE=plumed-common.dat
-be: METAD ARG=cv4 HEIGHT=0.5 SIGMA=0.3 PACE=500 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=200 BIASFACTOR=10 TEMP=300
+be: METAD ARG=cv4 HEIGHT=0.5 SIGMA=0.3 PACE=500 GRID_MIN=-pi GRID_MAX=pi BIASFACTOR=10
 PRINT ARG=cv1,cv2,cv3,cv4 STRIDE=1000 FILE=COLVAR
diff --git a/user-doc/tutorials/belfast-9a.txt b/user-doc/tutorials/belfast-9a.txt
index 639350a48201a7891a73574c50bb0708c448e9ab..f97fedd5e3bb210c7f733d04c29a4dcc09f5a5c1 100644
--- a/user-doc/tutorials/belfast-9a.txt
+++ b/user-doc/tutorials/belfast-9a.txt
@@ -18,7 +18,7 @@ The <a href="tutorial-resources/belfast-9a.tar.gz" download="belfast-9a.tar.gz">
 - system: the files use to generate the topol?.tpr files of the first and second example
 - first: an example on the use of chemical shifts as a collective variable
 - second: an example on the use of chemical shifts as replica-averaged restraints
-- third: an example on the use of RDCs (calculated with the theta-method) as replica-averaged restrains 
+- third: an example on the use of RDCs (calculated with the theta-method) as replica-averaged restraints 
 
 \section belfast-9-ins Instructions
 
@@ -27,20 +27,14 @@ The <a href="tutorial-resources/belfast-9a.tar.gz" download="belfast-9a.tar.gz">
 In the former tutorials it has been often discussed the possibility of measuring a distance with respect to a structure representing
 some kind of state for a system, i.e. \ref belfast-5. An alternative possibility is to use as a reference a set of experimental data
 that represent a state and measure the current deviation from the set. In plumed there are currently implemented the following NMR
-experimental observables: Chemical Shifts (only for proteins) \ref CS2BACKBONE and \ref CH3SHIFTS, \ref NOE distances and Residual Dipolar
-couplings \ref RDC. In addition \ref NOE collective variable can be also used for PRE distances and 3J Couplings can be implemented using
-\ref TORSION and \ref MATHEVAL. Among the above listed collective variables those based on chemical shifts make use of an external library, 
-ALMOST, that  must be downloaded and compiled separately. In addition plumed must be configured in such a way to link ALMOST. 
-Detailed instructions on how to compile PLUMED with ALMOST can be found in \ref CS2BACKBONE.
+experimental observables: Chemical Shifts (only for proteins) \ref CS2BACKBONE, \ref NOE distances, \ref JCOUPLING, \ref PRE intensities, 
+and Residual Dipolar couplings/pseudocontact shifts \ref RDC. 
 
-In the following we will write the CS2BACKBONE collective variable that has been used in Gratana et al. (2013).
+In the following we will write the \ref CS2BACKBONE collective variable that has been used in Gratana et al. (2013).
 
 \verbatim
 prot: GROUP ATOMS=1-862
-WHOLEMOLECULES ENTITY0=prot
-
-cs: CS2BACKBONE ATOMS=prot DATA=data FF=a03_gromacs.mdb NRES=56 FLAT=1.0 WRITE_CS=50 
-
+cs: CS2BACKBONE ATOMS=prot DATA=data NRES=56 CAMSHIFT 
 PRINT ARG=cs FILE=COLVAR STRIDE=100
 
 ENDPLUMED
@@ -52,13 +46,12 @@ folder (see first example in the resources tarball), one file for each nucleus.
 (i.e. CB of GLY) or where it has not been assigned. Additionally the data folder contains:
 
 - camshift.db: this file is a parameter file for camshift, it is a standard file needed to calculate the chemical shifts from a structure
-- a03_gromacs.mdb: this is a Amber force field in ALMOST format and it is used to map the atom names from plumed and almost (in this case we are using amber for our simulation)
 - template.pdb: this is a pdb file for the protein we are simulating (i.e. editconf -f conf.gro -o template.pdb) where atoms are ordered in the same way in which are included in the main code and again it is used to map the atom in plumed with those in almost.
 
 This example can be executed as
 
 \verbatim
-mdrun_mpi -s topol -plumed plumed
+gmx_mpi mdrun -s topol -plumed plumed
 \endverbatim
 
 \subsection belfast-9-replica Replica-Averaged Restrained Simulations 
@@ -70,14 +63,12 @@ is already a fortunate outcome. In order to increase the accuracy of a force fie
 to add to the force-field an additional term based on the agreement with a set of experimental data. This agreement is not enforced
 as a simple restraint because this would mean to ask the system to be always in agreement with all the experimental data at the
 same time, instead the restraint is applied over an AVERAGED COLLECTIVE VARIABLE where the average is performed over multiple
-identical simulations. In this way the is not a single replica that must be in agreement with the experimental data but they should
-be in agreement on average. It has been shown that this approach is equivalent in solving the problem of finding a modified
+ independent simulations of the same system in the same conditions. 
+In this way the is not a single replica that must be in agreement with the experimental data but they should
+be in agreement on average. It has been shown that this approach is equivalent to solving the problem of finding a modified
 version of the force field that will reproduce the provided set of experimental data withouth any additional assumption on the
 data themselves.
 
-Currently ENSEMBLE AVERAGING of a collective variable can be performed only using the NMR variables (\ref CS2BACKBONE, \ref CH3SHIFTS,
-\ref NOE and \ref RDC).
-
 The second example included in the resources show how the amber force field can be improved in the case of protein domain GB3 using
 the native state chemical shifts a replica-averaged restraint. By the fact that replica-averaging needs the use of multiple replica
 simulated in parallel in the same conditions it is easily complemented with BIAS-EXCHANGE or MULTIPLE WALKER metadynamics to enhance
@@ -85,38 +76,40 @@ the sampling.
 
 \verbatim
 prot: GROUP ATOMS=1-862
-WHOLEMOLECULES ENTITY0=prot
-
-cs: CS2BACKBONE ATOMS=prot DATA=data FF=a03_gromacs.mdb NRES=56 FLAT=0.0 WRITE_CS=500 ENSEMBLE
-
-cse: RESTRAINT ARG=cs AT=0. KAPPA=0. SLOPE=24
+cs: CS2BACKBONE ATOMS=prot DATA=data NRES=56
+enscs: ENSEMBLE ARG=(cs\.hn_.*),(cs\.nh_.*),(cs\.ca_.*),(cs\.cb_.*),(cs\.co_.*),(cs\.ha_.*)
+stcs: STATS ARG=enscs.* SQDEVSUM PARARG=(cs\.exphn_.*),(cs\.expnh_.*),(cs\.expca_.*),(cs\.expcb_.*),(cs\.expco_.*),(cs\.expha_.*)
+res: RESTRAINT ARG=stcs.sqdevsum AT=0. KAPPA=0. SLOPE=12
 
-PRINT ARG=cs FILE=COLVAR STRIDE=10
+PRINT ARG=(cs\.hn_.*),(cs\.nh_.*),(cs\.ca_.*),(cs\.cb_.*),(cs\.co_.*),(cs\.ha_.*) FILE=CS STRIDE=1000
+PRINT ARG=res.bias FILE=COLVAR STRIDE=10
 
 ENDPLUMED
 \endverbatim
 
-with respect to the case in which chemical shifts are used to define a standard collective variable, in this case the keyword ENSEMBLE
-tells plumed to calculate all the chemical shifts from the replicas (i.e. 4 replicas) average them and only after the averaging calculate
-the difference with respect to the experimental ones. On this difference that is the AVERAGED Collective Variable it is possible to apply
-a linear \ref RESTRAINT (because the variable is already a sum of squared differences) that is the new term we are adding to the underlying
-force field.
+with respect to the case in which chemical shifts are used to define a standard collective variable, in this case \ref CS2BACKBONE
+is a collective variable with multiple components, that are all the backcalculated chemical shifts, plus all the relative experimental
+values. The keyword function \ref ENSEMBLE tells plumed to calculate the average of the arguments over the replicas (i.e. 4 replicas) 
+and the function \ref STATS compare the averaged back calculated chemical shifts with the experimental values and calculates the sum
+of the squared deviation.
+On this latter number it is possible to apply a linear \ref RESTRAINT (because the variable is already a sum of squared differences) 
+that is the new term we are adding to the underlying force field.
 
 This example can be executed as
 \verbatim
-mpiexec -np 4 mdrun_mpi -s topol -plumed plumed -multi 4
+mpiexec -np 4 gmx_mpi mdrun -s topol -plumed plumed -multi 4
 \endverbatim
 
 The third example show how \ref RDC (calculated with the theta-methods) can be employed in the same way, in this case to describe the native state of Ubiquitin. In 
 particular it is possible to observe how the RDC averaged restraint applied on the correlation between the calculated and experimental 
-N-H and CA-HA RDCs result in the increase of the correlation of the RDCs for other bonds already on a very short time scale.
+N-H RDCs result in the increase of the correlation of the RDCs for other bonds already on a very short time scale.
 
 \verbatim
 RDC ...
-ENSEMBLE
-CORRELATION
 GYROM=-72.5388
-SCALE=0.001060 
+SCALE=0.001060
+ADDCOUPLINGS
+LABEL=nh 
 ATOMS1=20,21 COUPLING1=8.17
 ATOMS2=37,38 COUPLING2=-8.271
 ATOMS3=56,57 COUPLING3=-10.489
@@ -128,7 +121,7 @@ In this input the first four N-H RDCs are defined.
  
 This example can be executed as
 \verbatim
-mpiexec -np 8 mdrun_mpi -s topol -plumed plumed -multi 8
+mpiexec -np 8 gmx_mpi mdrun -s topol -plumed plumed -multi 8
 \endverbatim
 
 \section belfast-9-refer Reference
@@ -138,7 +131,7 @@ mpiexec -np 8 mdrun_mpi -s topol -plumed plumed -multi 8
 3. Camilloni, C., Cavalli, A. & Vendruscolo, M. Replica-Averaged Metadynamics. Journal of Chemical Theory … 9, 5610–5617 (2013).
 4. Roux, B. & Weare, J. On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method. J. Chem. Phys. 138, 084107 (2013).
 5. Boomsma, W., Lindorff-Larsen, K. & Ferkinghoff-Borg, J. Combining Experiments and Simulations Using the Maximum Entropy Principle. PLoS Comput. Biol. 10, e1003406 (2014).
-6. Camilloni, C. & Vendruscolo M. A Tensor-Free Method for the Structural and Dynamical Refinement of Proteins using Residual Dipolar Couplings. J. PHYS. CHEM. B XXX (2014).
+6. Camilloni, C. & Vendruscolo M. A Tensor-Free Method for the Structural and Dynamical Refinement of Proteins using Residual Dipolar Couplings. J. PHYS. CHEM. B 119, 653 (2015).
 
 */
 
diff --git a/user-doc/tutorials/belfast-9a/first/plumed.dat b/user-doc/tutorials/belfast-9a/first/plumed.dat
index 56cd466acf9376f58efa06acc1515ac30389f279..469e056523a89827752daa39f18b25f69cfd7629 100644
--- a/user-doc/tutorials/belfast-9a/first/plumed.dat
+++ b/user-doc/tutorials/belfast-9a/first/plumed.dat
@@ -1,7 +1,6 @@
 prot: GROUP ATOMS=1-862
-WHOLEMOLECULES ENTITY0=prot
 
-cs: CS2BACKBONE ATOMS=prot DATA=data FF=a03_gromacs.mdb NRES=56 FLAT=1.0 WRITE_CS=500
+cs: CS2BACKBONE ATOMS=prot DATA=data NRES=56 CAMSHIFT
 
 PRINT ARG=cs FILE=COLVAR STRIDE=10
 
diff --git a/user-doc/tutorials/belfast-9a/second/plumed.dat b/user-doc/tutorials/belfast-9a/second/plumed.dat
index 7ae31fbb9b9e76aefbd894762932a7121bbaf984..bb68ddd5273b4edb10ea3bf4003e4b4b50206589 100644
--- a/user-doc/tutorials/belfast-9a/second/plumed.dat
+++ b/user-doc/tutorials/belfast-9a/second/plumed.dat
@@ -1,10 +1,10 @@
 prot: GROUP ATOMS=1-862
-WHOLEMOLECULES ENTITY0=prot
+cs: CS2BACKBONE ATOMS=prot DATA=data NRES=56
+enscs: ENSEMBLE ARG=(cs\.hn_.*),(cs\.nh_.*),(cs\.ca_.*),(cs\.cb_.*),(cs\.co_.*),(cs\.ha_.*)
+stcs: STATS ARG=enscs.* SQDEVSUM PARARG=(cs\.exphn_.*),(cs\.expnh_.*),(cs\.expca_.*),(cs\.expcb_.*),(cs\.expco_.*),(cs\.expha_.*)
+res: RESTRAINT ARG=stcs.sqdevsum AT=0. KAPPA=0. SLOPE=12
 
-cs: CS2BACKBONE ATOMS=prot DATA=data FF=a03_gromacs.mdb NRES=56 FLAT=0.0 WRITE_CS=500 ENSEMBLE
-
-cse: RESTRAINT ARG=cs AT=0. KAPPA=0. SLOPE=24
-
-PRINT ARG=cs FILE=COLVAR STRIDE=10
+PRINT ARG=(cs\.hn_.*),(cs\.nh_.*),(cs\.ca_.*),(cs\.cb_.*),(cs\.co_.*),(cs\.ha_.*) FILE=CS STRIDE=1000
+PRINT ARG=res.bias FILE=COLVAR STRIDE=10
 
 ENDPLUMED
diff --git a/user-doc/tutorials/belfast-9a/third/plumed.dat b/user-doc/tutorials/belfast-9a/third/plumed.dat
index ea42d93f81dad9f61e9f086f2601b4f487922ced..de17ff543bdbb6dc1151c06443e3b3f21a58fa1b 100644
--- a/user-doc/tutorials/belfast-9a/third/plumed.dat
+++ b/user-doc/tutorials/belfast-9a/third/plumed.dat
@@ -1,8 +1,7 @@
 RDC ...
-ENSEMBLE
-CORRELATION
 GYROM=-72.5388
-SCALE=0.001060 
+SCALE=0.001060
+ADDCOUPLINGS 
 ATOMS1=20,21 COUPLING1=8.17
 ATOMS2=37,38 COUPLING2=-8.271
 ATOMS3=56,57 COUPLING3=-10.489
@@ -77,9 +76,8 @@ LABEL=nh
 
 RDC ...
 GYROM=179.9319
-ENSEMBLE
-CORRELATION
 SCALE=0.00125
+ADDCOUPLINGS
 ATOMS1=5,6 COUPLING1=-16.4200
 ATOMS2=22,23 COUPLING2=7.6090
 ATOMS3=39,40 COUPLING3=12.1850
@@ -148,8 +146,7 @@ LABEL=caha
 RDC ...
 GYROM=-18.2385
 SCALE=0.00117
-ENSEMBLE
-CORRELATION
+ADDCOUPLINGS
 ATOMS1=18,20 COUPLING1=-0.816
 ATOMS2=35,37 COUPLING2=2.106
 ATOMS3=54,56 COUPLING3=-0.142
@@ -223,8 +220,7 @@ LABEL=cn
 RDC ...
 GYROM=179.9319
 SCALE=0.00100
-ENSEMBLE
-CORRELATION
+ADDCOUPLINGS
 ATOMS1=18,21 COUPLING1=1.608
 ATOMS2=35,38 COUPLING2=-2.927
 ATOMS3=54,57 COUPLING3=2.066
@@ -295,10 +291,9 @@ LABEL=chn
 ... RDC
 
 RDC ...
-ENSEMBLE
-CORRELATION
 GYROM=45.2404
 SCALE=0.00115
+ADDCOUPLINGS
 ATOMS1=5,18 COUPLING1=-2.42
 ATOMS2=22,35 COUPLING2=0.613
 ATOMS3=39,54 COUPLING3=-1.055
@@ -367,10 +362,9 @@ LABEL=cac
 ... RDC
 
 RDC ...
-ENSEMBLE
-CORRELATION
 GYROM=45.2404
 SCALE=0.00105
+ADDCOUPLINGS
 ATOMS1=5,7 COUPLING1=1.6670
 ATOMS2=94,96 COUPLING2=2.0980
 ATOMS3=116,118 COUPLING3=1.5750
@@ -413,9 +407,23 @@ ATOMS39=1117,1119 COUPLING39=1.8100
 LABEL=cacb
 ... RDC
 
-rdce: RESTRAINT ARG=nh,caha KAPPA=0.,0. SLOPE=-5000.0,-5000 AT=1.,1.0
+enh: ENSEMBLE ARG=(nh\.rdc_.*)
+ecaha: ENSEMBLE ARG=(caha\.rdc_.*)
+ecn: ENSEMBLE ARG=(cn\.rdc_.*)
+echn: ENSEMBLE ARG=(chn\.rdc_.*)
+ecac: ENSEMBLE ARG=(cac\.rdc_.*)
+ecacb: ENSEMBLE ARG=(cacb\.rdc_.*)
 
-PRINT ARG=nh,caha,cn,chn,cac,cacb FILE=COLVAR STRIDE=20
+stnh: STATS ARG=enh.* PARARG=(nh\.exp_.*)
+stcaha: STATS ARG=ecaha.* PARARG=(caha\.exp_.*)
+stcn: STATS ARG=ecn.* PARARG=(cn\.exp_.*)
+stchn: STATS ARG=echn.* PARARG=(chn\.exp_.*)
+stcac: STATS ARG=ecac.* PARARG=(cac\.exp_.*)
+stcacb: STATS ARG=ecacb.* PARARG=(cacb\.exp_.*)
+
+rdce: RESTRAINT ARG=stnh.corr KAPPA=0. SLOPE=-500.0 AT=1.0
+
+PRINT ARG=stnh.corr,stcaha.corr,stcn.corr,stchn.corr,stcac.corr,stcacb.corr FILE=COLVAR STRIDE=20
 FLUSH STRIDE=40
 
 ENDPLUMED
diff --git a/user-doc/tutorials/cambridge.txt b/user-doc/tutorials/cambridge.txt
index fa2df772ed3f7d291ac65ca69b4fb654b7cc8c3b..ca3d2e7a471a902a63f90e75b32b083a85c86290 100644
--- a/user-doc/tutorials/cambridge.txt
+++ b/user-doc/tutorials/cambridge.txt
@@ -150,7 +150,7 @@ Once the PLUMED input file is prepared, one has to run Gromacs with the option t
 read the input file:
 
 \verbatim
-mdrun_mpi -plumed
+gmx_mpi mdrun -plumed
 \endverbatim
 
 During the metadynamics simulation, PLUMED will create two files, named COLVAR and HILLS.
@@ -359,7 +359,7 @@ The, in this case, two replicas start from the same GROMACS topology file replic
 Finally, GROMACS is launched as a parallel run on 4 cores, with one replica per core, with the command 
 
 \verbatim
-mpirun -np 4 mdrun_mpi -s topol -plumed plumed -multi 4 -replex 10000 >& log &
+mpirun -np 4 gmx_mpi mdrun -s topol -plumed plumed -multi 4 -replex 10000 >& log &
 \endverbatim
 
 where -replex 10000 indicates that every 10000 molecular-dynamics steps exchanges are attempted
diff --git a/user-doc/tutorials/cineca.txt b/user-doc/tutorials/cineca.txt
index 694a892024aac2e80216db1e80bbfe5ceb85b2d2..976c96c85790c42b2d29c57a474e05a950165ed9 100644
--- a/user-doc/tutorials/cineca.txt
+++ b/user-doc/tutorials/cineca.txt
@@ -91,7 +91,7 @@ that can be modified and used to generate a new .tpr file.
 
 GROMACS can be run (interactively) using the following command:
 \verbatim
-> mdrun_mpi -s ../SETUP/topolA.tpr -nsteps 10000 -x traj.xtc
+> gmx_mpi mdrun -s ../SETUP/topolA.tpr -nsteps 10000 -x traj.xtc
 \endverbatim
 The nsteps flags can be used to change the number of timesteps and topolA.tpr is the name of the tpr file.
 While running, GROMACS will produce a md.log file, with log information, and a traj.xtc file, with a binary trajectory.
@@ -102,7 +102,7 @@ The trajectory can be visualized with VMD using:
 
 To activate PLUMED during a GROMACS MD simulation, you need to add the -plumed flag
 \verbatim
-> mdrun_mpi -s ../SETUP/topolA.tpr -nsteps 10000 -plumed plumed.dat -x traj.xtc
+> gmx_mpi mdrun -s ../SETUP/topolA.tpr -nsteps 10000 -plumed plumed.dat -x traj.xtc
 \endverbatim
 Here plumed.dat is the name of the PLUMED input file. Notice that PLUMED will write
 information in the md.log that could be useful to verify if the simulation has been set up properly.
@@ -345,7 +345,7 @@ Once the PLUMED input file is prepared, one has to run GROMACS with the option t
 read the input file:
 
 \verbatim
-mdrun_mpi -s ../SETUP/topolA.tpr -plumed plumed.dat -nsteps 5000000 -x traj.xtc
+gmx_mpi mdrun -s ../SETUP/topolA.tpr -plumed plumed.dat -nsteps 5000000 -x traj.xtc
 \endverbatim
 
 During the metadynamics simulation, PLUMED will create two files, named COLVAR and HILLS.
@@ -679,7 +679,7 @@ several simultaneous simulations. This can be done with GROMACS using the
 multi replica framework. That is, if you have 4 tpr files named topol0.tpr,
 topol1.tpr, topol2.tpr, topol3.tpr you can run 4 simultaneous simulations.
 \verbatim
-> mpirun -np 4 mdrun_mpi -s topol.tpr -plumed plumed.dat -multi 4 -nsteps 500000
+> mpirun -np 4 gmx_mpi mdrun -s topol.tpr -plumed plumed.dat -multi 4 -nsteps 500000
 \endverbatim
 Each of the 4 replicas will open a different topol file, and GROMACS will
 take care of adding the replica number before the .tpr suffix.
@@ -805,7 +805,7 @@ done
 And then run GROMACS with the following command: 
 
 \verbatim
-mpirun -np 32 mdrun_mpi -plumed plumed.dat -s topol.tpr -multi 32 -replex 1000 -nsteps 500000 -x traj.xtc
+mpirun -np 32 gmx_mpi mdrun -plumed plumed.dat -s topol.tpr -multi 32 -replex 1000 -nsteps 500000 -x traj.xtc
 \endverbatim
 
 To be able to combine data from all the simulations, it is necessary to have an overlap between 
diff --git a/user-doc/tutorials/hrex.txt b/user-doc/tutorials/hrex.txt
index b3c4f6f754d853899499e9a9d5c3401f9f41d8a1..f62b22bc1c1c240570704cfa07880a5228054a7b 100644
--- a/user-doc/tutorials/hrex.txt
+++ b/user-doc/tutorials/hrex.txt
@@ -125,7 +125,7 @@ do
 # -maxwarn is often needed because box could be charged
   grompp_mpi_d  -maxwarn 1 -o topol$i.tpr -f grompp$i.mdp -p topol$i.top
 done
-mpirun -np $nrep mdrun_mpi_d -v -plumed plumed.dat -multi $nrep -replex 100 -nsteps 15000000 -hrex
+mpirun -np $nrep gmx_mpi mdrun_d -v -plumed plumed.dat -multi $nrep -replex 100 -nsteps 15000000 -hrex
 \endverbatim
 
 Notice that total cell could be charged. This happens whenever the scaled portion of the system
diff --git a/user-doc/tutorials/munster.txt b/user-doc/tutorials/munster.txt
index 6de5b465d39c554616c413105503c191cd0db32c..98efd99a217a54a350754a43f8a9e7b6a3bcb555 100644
--- a/user-doc/tutorials/munster.txt
+++ b/user-doc/tutorials/munster.txt
@@ -90,7 +90,7 @@ namely:
 
 Gromacs md can be run using on the command line:
 \verbatim
-> mdrun_mpi -s topolA.tpr -nsteps 10000
+> gmx_mpi mdrun -s topolA.tpr -nsteps 10000
 \endverbatim
 The nsteps flags can be used to change the number of timesteps and topolA.tpr is the name of the tpr file.
 While running, gromacs will produce an md.log file, with log information, and a traj.xtc file, with a binary trajectory.
@@ -101,7 +101,7 @@ The trajectory can be visualized with VMD using a command such as
 
 To run a simulation with gromacs+plumed you just need to add a -plumed flag
 \verbatim
-> mdrun_mpi -s topolA.tpr -nsteps 10000 -plumed plumed.dat
+> gmx_mpi mdrun -s topolA.tpr -nsteps 10000 -plumed plumed.dat
 \endverbatim
 Here plumed.dat is the name of the plumed input file. Notice that PLUMED will write
 information in the md.log that could be useful to verify if the simulation has been set up properly.
@@ -490,7 +490,7 @@ Once the PLUMED input file is prepared, one has to run Gromacs with the option t
 read the input file:
 
 \verbatim
-mdrun_mpi -s ../TOPO/topolA.tpr -plumed plumed.dat -nsteps 5000000
+gmx_mpi mdrun -s ../TOPO/topolA.tpr -plumed plumed.dat -nsteps 5000000
 \endverbatim
 
 During the metadynamics simulation, PLUMED will create two files, named COLVAR and HILLS.
@@ -656,7 +656,7 @@ Once the PLUMED input file is prepared, one has to run Gromacs with the option t
 read the input file:
 
 \verbatim
-mdrun_mpi -s ../TOPO/topolA.tpr -plumed plumed.dat -nsteps 5000000
+gmx_mpi mdrun -s ../TOPO/topolA.tpr -plumed plumed.dat -nsteps 5000000
 \endverbatim
 
 As we did in the previous exercise, we can use COLVAR to visualize the behavior of the CV during the simulation.
@@ -861,7 +861,7 @@ several simultaneous simulations. This can be done with gromacs using the
 multi replica framework. That is, if you have 4 tpr files named topol0.tpr,
 topol1.tpr, topol2.tpr, topol3.tpr you can run 4 simultaneous simulations.
 \verbatim
-> mpirun -np 4 mdrun_mpi -s topol.tpr -plumed plumed.dat -multi 4 -nsteps 500000
+> mpirun -np 4 gmx_mpi mdrun -s topol.tpr -plumed plumed.dat -multi 4 -nsteps 500000
 \endverbatim
 Each of the 4 replicas will open a different topol file, and GROMACS will
 take care of adding the replica number before the .tpr suffix.
@@ -983,7 +983,7 @@ fi
 done
 
 # run REM
-mpirun -np $nrep mdrun_mpi -plumed plumed.dat -s topol.tpr -multi $nrep -replex 1000 -nsteps 500000
+mpirun -np $nrep gmx_mpi mdrun -plumed plumed.dat -s topol.tpr -multi $nrep -replex 1000 -nsteps 500000
 \endverbatim
 
 To be able to combine data from all the simulations, it is necessary to have an overlap between