Merge branch 'randorien' of https://github.com/haddocking/haddock3 into randorien

Author: amjjbonvin

CHANGELOG.md

@@ -1,6 +1,7 @@
 # Changelog
 
 - 2026-04-14: Implemented separate control of separation and randome rotations of molecules - Issue #1491
+- 2026-04-14: Increase max number of timesteps in openmm module - BioExcel forum 6072
 - 2026-04-12: Add possibility to run MD (mdref, mdscoring) without solvent - Issue #1512
 - 2026-04-10: Corrected the definition of ion restraints in flexref - Issue #1510
 - 2026-04-10: Removing analysis modules downstream when restarting - Issue #1495

examples/docking-protein-ligand-centered/docking-protein-ligand-centered-test.cfg

@@ -21,6 +21,7 @@ autohis = true
 [rigidbody]
 sampling = 5
 tolerance = 20
+# Setting the `separate` parameter to false to keep the ligand in the binding site
 separate = false
 randrot = true
 ambig_fname = "./data/ambig_active.tbl"

examples/docking-protein-ligand-centered/docking-protein-ligand-centered.cfg

@@ -20,6 +20,7 @@ delenph = false
 [rigidbody]
 sampling = 1000
 tolerance = 5
+# Setting the `separate` parameter to false to keep the ligand in the binding site
 separate = false
 randrot = true
 ambig_fname = "./data/ambig_active.tbl"

src/haddock/modules/refinement/openmm/defaults.yaml

@@ -137,8 +137,8 @@ equilibration_timesteps:
 simulation_timesteps:
   default: 2000
   type: integer
-  min: 0
-  max: 1000000
+  min: 0 
+  max: 10000000
   title: Simulation timesteps.
   short: Simulation timesteps performed during the simulation.
   long: Simulation timesteps performed during the simulation.

src/haddock/modules/sampling/rigidbody/defaults.yaml

@@ -856,7 +856,7 @@ separate:
   title: Separate molecules
   short: Translate molecules to separate them
   long: Translate molecules to separate them ensuring a minimum distance
-    that allows rotation without clashes
+    that allows rotations (controlled by the randrot parameter) without clashes
   group: 'sampling'
   explevel: easy
 randrot: