Fix issue #202

CHANGELOG.md

@@ -19,9 +19,11 @@ Changelog
 * Skip minimisation on restart [#191](https://github.com/OpenBioSim/somd2/pull/191).
 * Pre-equilibrate the water with GCMC moves before minimising in the regular `Runner`, making it consistent with the `RepexRunner`, which already did so to stop the geometry relaxing into a dry pocket [#191](https://github.com/OpenBioSim/somd2/pull/191).
 * Add a `precision` option for GPU platforms, defaulting to `mixed` [#191](https://github.com/OpenBioSim/somd2/pull/191).
-* Add support for generating Morse restraints for ring-breaking perturbations.
-* Remove the unused `kappa` lever equations from the ring-breaking/making lambda schedules.
-* Account for off-site charges (virtual sites) when computing the charge difference between the end states. They are held as a molecule property rather than on the atoms, so a charge-preserving perturbation could appear to change charge and be given spurious alchemical ions.
+* Add support for generating Morse restraints for ring-breaking perturbations [#194](https://github.com/OpenBioSim/somd2/pull/194).
+* Remove the unused `kappa` lever equations from the ring-breaking/making lambda schedules [#195](https://github.com/OpenBioSim/somd2/pull/195).
+* Accept stream file paths for the `restraints` and `lambda_schedule` configuration options, so they can be set from the command line [#198](https://github.com/OpenBioSim/somd2/pull/198).
+* Account for off-site charges (virtual sites) when computing the charge difference between the end states. They are held as a molecule property rather than on the atoms, so a charge-preserving perturbation could appear to change charge and be given spurious alchemical ions [#200](https://github.com/OpenBioSim/somd2/pull/200).
+* Handle `num_lambda=1`, which previously raised a `ZeroDivisionError` when generating the lambda values. The `RepexRunner` now rejects a single lambda window, since there is nothing to exchange with and the regular `Runner` is faster [#203](https://github.com/OpenBioSim/somd2/pull/203).
 
 [2026.1.0](https://github.com/openbiosim/somd2/compare/2025.1.0...2026.1.0) - Jun 2026
 --------------------------------------------------------------------------------------

src/somd2/runner/_base.py

@@ -466,6 +466,8 @@ def __init__(self, system, config):
         # Set the lambda values.
         if self._config.lambda_values:
             self._lambda_values = self._config.lambda_values
+        elif self._config.num_lambda == 1:
+            self._lambda_values = [0.0]
         else:
             self._lambda_values = [
                 round(i / (self._config.num_lambda - 1), 5)

src/somd2/runner/_repex.py

@@ -1233,6 +1233,16 @@ def __init__(self, system, config):
         # fewer slots than replicas, each slot is re-used to propagate several
         # replicas per cycle, changing its lambda value as it goes.
         self._num_replicas = len(self._lambda_values)
+
+        # There is nothing to exchange with a single replica.
+        if self._num_replicas < 2:
+            msg = (
+                "Replica exchange requires at least two "
+                f"{_lam_sym} values. Please use the Runner class instead."
+            )
+            _logger.error(msg)
+            raise ValueError(msg)
+
         self._set_num_slots()
 
         # Auto-generate a Boresch restraint for ABFE runs with no user-supplied
@@ -3068,7 +3078,7 @@ def _save_transition_matrix(self):
                         swaps[i_state, j_state] + swaps[j_state, i_state]
                     ) / denom
             else:
-                t[i_state, i_state] = 1.0
+                t_ij[i_state, i_state] = 1.0
 
         # Backup the existing transition matrix, if it exists.
         if self._repex_matrix.exists():