diff --git a/regtest/crystallization/rt-env-sim/rt-bcc/COLVAR.reference b/regtest/crystallization/rt-env-sim-bcc/COLVAR.reference
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-bcc/COLVAR.reference
rename to regtest/crystallization/rt-env-sim-bcc/COLVAR.reference
diff --git a/regtest/crystallization/rt-env-sim-bcc/Makefile b/regtest/crystallization/rt-env-sim-bcc/Makefile
new file mode 100644
index 0000000000..3703b27cea
--- /dev/null
+++ b/regtest/crystallization/rt-env-sim-bcc/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-bcc/bcc.pdb b/regtest/crystallization/rt-env-sim-bcc/bcc.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-bcc/bcc.pdb
rename to regtest/crystallization/rt-env-sim-bcc/bcc.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-bcc/config b/regtest/crystallization/rt-env-sim-bcc/config
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-bcc/config
rename to regtest/crystallization/rt-env-sim-bcc/config
diff --git a/regtest/crystallization/rt-env-sim/rt-bcc/plumed.dat b/regtest/crystallization/rt-env-sim-bcc/plumed.dat
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-bcc/plumed.dat
rename to regtest/crystallization/rt-env-sim-bcc/plumed.dat
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-1env/COLVAR.reference b/regtest/crystallization/rt-env-sim-custom-1env/COLVAR.reference
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-1env/COLVAR.reference
rename to regtest/crystallization/rt-env-sim-custom-1env/COLVAR.reference
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-1env/IceIh.pdb b/regtest/crystallization/rt-env-sim-custom-1env/IceIh.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-1env/IceIh.pdb
rename to regtest/crystallization/rt-env-sim-custom-1env/IceIh.pdb
diff --git a/regtest/crystallization/rt-env-sim-custom-1env/Makefile b/regtest/crystallization/rt-env-sim-custom-1env/Makefile
new file mode 100644
index 0000000000..3703b27cea
--- /dev/null
+++ b/regtest/crystallization/rt-env-sim-custom-1env/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-1env/config b/regtest/crystallization/rt-env-sim-custom-1env/config
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-1env/config
rename to regtest/crystallization/rt-env-sim-custom-1env/config
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-1env/env1.pdb b/regtest/crystallization/rt-env-sim-custom-1env/env1.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-1env/env1.pdb
rename to regtest/crystallization/rt-env-sim-custom-1env/env1.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-1env/plumed.dat b/regtest/crystallization/rt-env-sim-custom-1env/plumed.dat
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-1env/plumed.dat
rename to regtest/crystallization/rt-env-sim-custom-1env/plumed.dat
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-multienv/COLVAR.reference b/regtest/crystallization/rt-env-sim-custom-multienv/COLVAR.reference
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-multienv/COLVAR.reference
rename to regtest/crystallization/rt-env-sim-custom-multienv/COLVAR.reference
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-multienv/IceIh.pdb b/regtest/crystallization/rt-env-sim-custom-multienv/IceIh.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-multienv/IceIh.pdb
rename to regtest/crystallization/rt-env-sim-custom-multienv/IceIh.pdb
diff --git a/regtest/crystallization/rt-env-sim-custom-multienv/Makefile b/regtest/crystallization/rt-env-sim-custom-multienv/Makefile
new file mode 100644
index 0000000000..3703b27cea
--- /dev/null
+++ b/regtest/crystallization/rt-env-sim-custom-multienv/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-multienv/config b/regtest/crystallization/rt-env-sim-custom-multienv/config
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-multienv/config
rename to regtest/crystallization/rt-env-sim-custom-multienv/config
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-multienv/env1.pdb b/regtest/crystallization/rt-env-sim-custom-multienv/env1.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-multienv/env1.pdb
rename to regtest/crystallization/rt-env-sim-custom-multienv/env1.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-multienv/env2.pdb b/regtest/crystallization/rt-env-sim-custom-multienv/env2.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-multienv/env2.pdb
rename to regtest/crystallization/rt-env-sim-custom-multienv/env2.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-multienv/env3.pdb b/regtest/crystallization/rt-env-sim-custom-multienv/env3.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-multienv/env3.pdb
rename to regtest/crystallization/rt-env-sim-custom-multienv/env3.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-multienv/env4.pdb b/regtest/crystallization/rt-env-sim-custom-multienv/env4.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-multienv/env4.pdb
rename to regtest/crystallization/rt-env-sim-custom-multienv/env4.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-multienv/plumed.dat b/regtest/crystallization/rt-env-sim-custom-multienv/plumed.dat
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-custom-multienv/plumed.dat
rename to regtest/crystallization/rt-env-sim-custom-multienv/plumed.dat
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv-multienv/IceIh.pdb b/regtest/crystallization/rt-env-sim-deriv-multienv/IceIh.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv-multienv/IceIh.pdb
rename to regtest/crystallization/rt-env-sim-deriv-multienv/IceIh.pdb
diff --git a/regtest/crystallization/rt-env-sim-deriv-multienv/Makefile b/regtest/crystallization/rt-env-sim-deriv-multienv/Makefile
new file mode 100644
index 0000000000..3703b27cea
--- /dev/null
+++ b/regtest/crystallization/rt-env-sim-deriv-multienv/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv-multienv/config b/regtest/crystallization/rt-env-sim-deriv-multienv/config
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv-multienv/config
rename to regtest/crystallization/rt-env-sim-deriv-multienv/config
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv-multienv/deriv.reference b/regtest/crystallization/rt-env-sim-deriv-multienv/deriv.reference
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv-multienv/deriv.reference
rename to regtest/crystallization/rt-env-sim-deriv-multienv/deriv.reference
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv-multienv/env1.pdb b/regtest/crystallization/rt-env-sim-deriv-multienv/env1.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv-multienv/env1.pdb
rename to regtest/crystallization/rt-env-sim-deriv-multienv/env1.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv-multienv/env2.pdb b/regtest/crystallization/rt-env-sim-deriv-multienv/env2.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv-multienv/env2.pdb
rename to regtest/crystallization/rt-env-sim-deriv-multienv/env2.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv-multienv/env3.pdb b/regtest/crystallization/rt-env-sim-deriv-multienv/env3.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv-multienv/env3.pdb
rename to regtest/crystallization/rt-env-sim-deriv-multienv/env3.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv-multienv/env4.pdb b/regtest/crystallization/rt-env-sim-deriv-multienv/env4.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv-multienv/env4.pdb
rename to regtest/crystallization/rt-env-sim-deriv-multienv/env4.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv-multienv/plumed.dat b/regtest/crystallization/rt-env-sim-deriv-multienv/plumed.dat
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv-multienv/plumed.dat
rename to regtest/crystallization/rt-env-sim-deriv-multienv/plumed.dat
diff --git a/regtest/crystallization/rt-env-sim-deriv/Makefile b/regtest/crystallization/rt-env-sim-deriv/Makefile
new file mode 100644
index 0000000000..3703b27cea
--- /dev/null
+++ b/regtest/crystallization/rt-env-sim-deriv/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv/bcc.pdb b/regtest/crystallization/rt-env-sim-deriv/bcc.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv/bcc.pdb
rename to regtest/crystallization/rt-env-sim-deriv/bcc.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv/config b/regtest/crystallization/rt-env-sim-deriv/config
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv/config
rename to regtest/crystallization/rt-env-sim-deriv/config
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv/deriv.reference b/regtest/crystallization/rt-env-sim-deriv/deriv.reference
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv/deriv.reference
rename to regtest/crystallization/rt-env-sim-deriv/deriv.reference
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv/plumed.dat b/regtest/crystallization/rt-env-sim-deriv/plumed.dat
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-deriv/plumed.dat
rename to regtest/crystallization/rt-env-sim-deriv/plumed.dat
diff --git a/regtest/crystallization/rt-env-sim/rt-diamond/COLVAR.reference b/regtest/crystallization/rt-env-sim-diamond/COLVAR.reference
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-diamond/COLVAR.reference
rename to regtest/crystallization/rt-env-sim-diamond/COLVAR.reference
diff --git a/regtest/crystallization/rt-env-sim-diamond/Makefile b/regtest/crystallization/rt-env-sim-diamond/Makefile
new file mode 100644
index 0000000000..3703b27cea
--- /dev/null
+++ b/regtest/crystallization/rt-env-sim-diamond/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-diamond/config b/regtest/crystallization/rt-env-sim-diamond/config
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-diamond/config
rename to regtest/crystallization/rt-env-sim-diamond/config
diff --git a/regtest/crystallization/rt-env-sim/rt-diamond/diamond.pdb b/regtest/crystallization/rt-env-sim-diamond/diamond.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-diamond/diamond.pdb
rename to regtest/crystallization/rt-env-sim-diamond/diamond.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-diamond/plumed.dat b/regtest/crystallization/rt-env-sim-diamond/plumed.dat
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-diamond/plumed.dat
rename to regtest/crystallization/rt-env-sim-diamond/plumed.dat
diff --git a/regtest/crystallization/rt-env-sim/rt-fcc/COLVAR.reference b/regtest/crystallization/rt-env-sim-fcc/COLVAR.reference
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-fcc/COLVAR.reference
rename to regtest/crystallization/rt-env-sim-fcc/COLVAR.reference
diff --git a/regtest/crystallization/rt-env-sim-fcc/Makefile b/regtest/crystallization/rt-env-sim-fcc/Makefile
new file mode 100644
index 0000000000..3703b27cea
--- /dev/null
+++ b/regtest/crystallization/rt-env-sim-fcc/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-fcc/config b/regtest/crystallization/rt-env-sim-fcc/config
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-fcc/config
rename to regtest/crystallization/rt-env-sim-fcc/config
diff --git a/regtest/crystallization/rt-env-sim/rt-fcc/fcc.pdb b/regtest/crystallization/rt-env-sim-fcc/fcc.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-fcc/fcc.pdb
rename to regtest/crystallization/rt-env-sim-fcc/fcc.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-fcc/plumed.dat b/regtest/crystallization/rt-env-sim-fcc/plumed.dat
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-fcc/plumed.dat
rename to regtest/crystallization/rt-env-sim-fcc/plumed.dat
diff --git a/regtest/crystallization/rt-env-sim/rt-hcp/COLVAR.reference b/regtest/crystallization/rt-env-sim-hcp/COLVAR.reference
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-hcp/COLVAR.reference
rename to regtest/crystallization/rt-env-sim-hcp/COLVAR.reference
diff --git a/regtest/crystallization/rt-env-sim-hcp/Makefile b/regtest/crystallization/rt-env-sim-hcp/Makefile
new file mode 100644
index 0000000000..3703b27cea
--- /dev/null
+++ b/regtest/crystallization/rt-env-sim-hcp/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-hcp/config b/regtest/crystallization/rt-env-sim-hcp/config
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-hcp/config
rename to regtest/crystallization/rt-env-sim-hcp/config
diff --git a/regtest/crystallization/rt-env-sim/rt-hcp/hcp.pdb b/regtest/crystallization/rt-env-sim-hcp/hcp.pdb
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-hcp/hcp.pdb
rename to regtest/crystallization/rt-env-sim-hcp/hcp.pdb
diff --git a/regtest/crystallization/rt-env-sim/rt-hcp/plumed.dat b/regtest/crystallization/rt-env-sim-hcp/plumed.dat
similarity index 100%
rename from regtest/crystallization/rt-env-sim/rt-hcp/plumed.dat
rename to regtest/crystallization/rt-env-sim-hcp/plumed.dat
diff --git a/regtest/crystallization/rt-env-sim/rt-bcc/Makefile b/regtest/crystallization/rt-env-sim/rt-bcc/Makefile
deleted file mode 100644
index ffb048e678..0000000000
--- a/regtest/crystallization/rt-env-sim/rt-bcc/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-1env/Makefile b/regtest/crystallization/rt-env-sim/rt-custom-1env/Makefile
deleted file mode 100644
index ffb048e678..0000000000
--- a/regtest/crystallization/rt-env-sim/rt-custom-1env/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-custom-multienv/Makefile b/regtest/crystallization/rt-env-sim/rt-custom-multienv/Makefile
deleted file mode 100644
index ffb048e678..0000000000
--- a/regtest/crystallization/rt-env-sim/rt-custom-multienv/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv-multienv/Makefile b/regtest/crystallization/rt-env-sim/rt-deriv-multienv/Makefile
deleted file mode 100644
index ffb048e678..0000000000
--- a/regtest/crystallization/rt-env-sim/rt-deriv-multienv/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-deriv/Makefile b/regtest/crystallization/rt-env-sim/rt-deriv/Makefile
deleted file mode 100644
index ffb048e678..0000000000
--- a/regtest/crystallization/rt-env-sim/rt-deriv/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-diamond/Makefile b/regtest/crystallization/rt-env-sim/rt-diamond/Makefile
deleted file mode 100644
index ffb048e678..0000000000
--- a/regtest/crystallization/rt-env-sim/rt-diamond/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-fcc/Makefile b/regtest/crystallization/rt-env-sim/rt-fcc/Makefile
deleted file mode 100644
index ffb048e678..0000000000
--- a/regtest/crystallization/rt-env-sim/rt-fcc/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../../../scripts/test.make
diff --git a/regtest/crystallization/rt-env-sim/rt-hcp/Makefile b/regtest/crystallization/rt-env-sim/rt-hcp/Makefile
deleted file mode 100644
index ffb048e678..0000000000
--- a/regtest/crystallization/rt-env-sim/rt-hcp/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../../../scripts/test.make