diff --git a/src/haddock/modules/refinement/emref/defaults.yaml b/src/haddock/modules/refinement/emref/defaults.yaml
index 136d320d2..95c11fefd 100644
--- a/src/haddock/modules/refinement/emref/defaults.yaml
+++ b/src/haddock/modules/refinement/emref/defaults.yaml
@@ -1391,7 +1391,7 @@ keepwater:
   group: 'sampling'
   explevel: guru
 tolerance:
-  default: 0
+  default: 5
   type: integer
   min: 0
   max: 99
diff --git a/src/haddock/modules/sampling/rigidbody/defaults.yaml b/src/haddock/modules/sampling/rigidbody/defaults.yaml
index b0c29f5b6..ff3a35dd9 100644
--- a/src/haddock/modules/sampling/rigidbody/defaults.yaml
+++ b/src/haddock/modules/sampling/rigidbody/defaults.yaml
@@ -900,7 +900,7 @@ inter_rigid:
   group: 'sampling'
   explevel: expert
 tolerance:
-  default: 0
+  default: 5
   type: integer
   min: 0
   max: 99
diff --git a/src/haddock/modules/scoring/emscoring/defaults.yaml b/src/haddock/modules/scoring/emscoring/defaults.yaml
index bc54ef51b..a4ac2e233 100644
--- a/src/haddock/modules/scoring/emscoring/defaults.yaml
+++ b/src/haddock/modules/scoring/emscoring/defaults.yaml
@@ -277,7 +277,7 @@ nemsteps:
   group: 'sampling'
   explevel: expert
 tolerance:
-  default: 0
+  default: 5
   type: integer
   min: 0
   max: 99