diff --git a/regtest/rt35/config b/regtest/rt35/config
index 45386cb93cee6467a71b54d79286cad0b809621b..ec1203c7a251c0c8f49996510c1ece9bddfb4b4f 100644
--- a/regtest/rt35/config
+++ b/regtest/rt35/config
@@ -1,2 +1,4 @@
 type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz ../../trajectories/diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../trajectories/diala_traj_nm.xyz ../trajectories/path_msd/frame_1.dat ../trajectories/path_msd/frame_21.dat ../trajectories/path_msd/frame_42.dat " 
+
diff --git a/regtest/rt35/plumed.dat b/regtest/rt35/plumed.dat
index 327e58458a77bd29ec5276a08200ac623b196ddd..08006d14c097f5041f23da9ef7f70ac1bfb3d933 100644
--- a/regtest/rt35/plumed.dat
+++ b/regtest/rt35/plumed.dat
@@ -1,6 +1,6 @@
-t1: RMSD REFERENCE=../../trajectories/path_msd/frame_1.dat TYPE=OPTIMAL SQUARED
-t2: RMSD REFERENCE=../../trajectories/path_msd/frame_21.dat TYPE=OPTIMAL SQUARED 
-t3: RMSD REFERENCE=../../trajectories/path_msd/frame_42.dat TYPE=OPTIMAL SQUARED
+t1: RMSD REFERENCE=frame_1.dat TYPE=OPTIMAL SQUARED
+t2: RMSD REFERENCE=frame_21.dat TYPE=OPTIMAL SQUARED 
+t3: RMSD REFERENCE=frame_42.dat TYPE=OPTIMAL SQUARED
 p2: FUNCPATHMSD ARG=t1,t2,t3 LAMBDA=500.0 
 PRINT ARG=t1,t2,t3,p2.s,p2.z STRIDE=1 FILE=colvar FMT=%8.4f
 DUMPDERIVATIVES ARG=p2.s,p2.z STRIDE=1 FILE=deriv FMT=%8.4f
diff --git a/regtest/rt37/config b/regtest/rt37/config
index 45386cb93cee6467a71b54d79286cad0b809621b..e53299d7ac1546297337d98959ebb12cd3ddabf3 100644
--- a/regtest/rt37/config
+++ b/regtest/rt37/config
@@ -1,2 +1,3 @@
 type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz ../../trajectories/diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../trajectories/diala_traj_nm.xyz ../trajectories/path_msd/frame_1.dat ../trajectories/path_msd/frame_21.dat ../trajectories/path_msd/frame_42.dat " 
diff --git a/regtest/rt37/plumed.dat b/regtest/rt37/plumed.dat
index 94aa01be34414d85cb948121aeade896ff5d1023..f84f21d1aa8b5c04dd1b58a5b0b147296075fd5c 100644
--- a/regtest/rt37/plumed.dat
+++ b/regtest/rt37/plumed.dat
@@ -1,6 +1,6 @@
-t1: RMSD REFERENCE=../../trajectories/path_msd/frame_1.dat TYPE=OPTIMAL SQUARED
-t2: RMSD REFERENCE=../../trajectories/path_msd/frame_21.dat TYPE=OPTIMAL SQUARED 
-t3: RMSD REFERENCE=../../trajectories/path_msd/frame_42.dat TYPE=OPTIMAL SQUARED
+t1: RMSD REFERENCE=frame_1.dat TYPE=OPTIMAL SQUARED
+t2: RMSD REFERENCE=frame_21.dat TYPE=OPTIMAL SQUARED 
+t3: RMSD REFERENCE=frame_42.dat TYPE=OPTIMAL SQUARED
 p2: FUNCPATHMSD ARG=t1,t2,t3 LAMBDA=500.0  NEIGH_STRIDE=0.2 NEIGH_SIZE=2  
 PRINT ARG=t1,t2,t3,p2.s,p2.z STRIDE=1 FILE=colvar FMT=%8.4f
 DUMPDERIVATIVES ARG=p2.s,p2.z STRIDE=1 FILE=deriv FMT=%8.4f
diff --git a/regtest/rt38/config b/regtest/rt38/config
index 45386cb93cee6467a71b54d79286cad0b809621b..623857a994b5965fb24c45eb0e6e20c71c6722e9 100644
--- a/regtest/rt38/config
+++ b/regtest/rt38/config
@@ -1,2 +1,3 @@
 type=driver
-arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz ../../trajectories/diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 10 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../trajectories/diala_traj_nm.xyz ../trajectories/path_msd/frame_1.dat "  
diff --git a/regtest/rt38/plumed.dat b/regtest/rt38/plumed.dat
index f6199a0178ff3587b8e3db6071eeac18ac769000..9a8ebb3f72e801aab49a8d8daf54c1e8899da6af 100644
--- a/regtest/rt38/plumed.dat
+++ b/regtest/rt38/plumed.dat
@@ -1,4 +1,4 @@
-t1: RMSD REFERENCE=../../trajectories/path_msd/frame_1.dat TYPE=OPTIMAL SQUARED
+t1: RMSD REFERENCE=frame_1.dat TYPE=OPTIMAL SQUARED
 MOVINGRESTRAINT ...
  ARG=t1
  STEP0=0      AT0=1.  KAPPA0=100.0
diff --git a/regtest/rt39/config b/regtest/rt39/config
index a7b263882c01e2264ecf63e41867bc66e65a6522..1a76fc9e16ffafb14a361e401b8fafaa9d3371c1 100644
--- a/regtest/rt39/config
+++ b/regtest/rt39/config
@@ -1,2 +1,3 @@
 type=driver
-arg="--plumed plumed.dat --stride 50 --timestep 0.005 --ixyz ../../trajectories/diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../trajectories/diala_traj_nm.xyz  ../trajectories/path_msd/all.pdb "
diff --git a/regtest/rt39/plumed.dat b/regtest/rt39/plumed.dat
index 05a2a2444e2b26a5849e75633aa92cd45d9cbffc..b88c67d6e913f08dacaa726680d7952dcf7d79f8 100644
--- a/regtest/rt39/plumed.dat
+++ b/regtest/rt39/plumed.dat
@@ -1,4 +1,4 @@
-p2: PATHMSD REFERENCE=../../trajectories/path_msd/all.pdb LAMBDA=69087    
-p3: PATHMSD REFERENCE=../../trajectories/path_msd/all.pdb LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=0.2
+p2: PATHMSD REFERENCE=all.pdb LAMBDA=69087    
+p3: PATHMSD REFERENCE=all.pdb LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=0.2
 PRINT ARG=p2.sss,p2.zzz,p3.sss,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
 DUMPDERIVATIVES ARG=p2.sss,p2.zzz,p3.sss,p3.zzz STRIDE=1 FILE=deriv
diff --git a/regtest/rt40/config b/regtest/rt40/config
index a7b263882c01e2264ecf63e41867bc66e65a6522..c5f67be26f899e3fb97383c69b6ff651e5744ab3 100644
--- a/regtest/rt40/config
+++ b/regtest/rt40/config
@@ -1,2 +1,3 @@
 type=driver
-arg="--plumed plumed.dat --stride 50 --timestep 0.005 --ixyz ../../trajectories/diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+arg="--plumed plumed.dat --stride 50 --timestep 0.005 --ixyz diala_traj_nm.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../trajectories/diala_traj_nm.xyz  ../trajectories/path_msd/allv.pdb "
diff --git a/regtest/rt40/plumed.dat b/regtest/rt40/plumed.dat
index a40af9f50804c82428c19546ad92862bc0febabf..38ef8ed3640b224f002e62cb97112927c8d5b26b 100644
--- a/regtest/rt40/plumed.dat
+++ b/regtest/rt40/plumed.dat
@@ -1,4 +1,4 @@
-p2: PROPERTYMAP REFERENCE=../../trajectories/path_msd/allv.pdb PROPERTY=X,Y LAMBDA=69087    
-p3: PROPERTYMAP REFERENCE=../../trajectories/path_msd/allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=0.2
+p2: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087    
+p3: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=0.2
 PRINT ARG=p2.X,p2.Y,p2.zzz,p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
 DUMPDERIVATIVES ARG=p2.X,p2.Y,p2.zzz,p3.X,p3.Y,p3.zzz STRIDE=1 FILE=deriv