diff --git a/src/somd2/config/_config.py b/src/somd2/config/_config.py
index a799f63..21b2c15 100644
--- a/src/somd2/config/_config.py
+++ b/src/somd2/config/_config.py
@@ -134,6 +134,7 @@ def __init__(
         opencl_platform_index=0,
         oversubscription_factor=1,
         replica_exchange=False,
+        randomise_velocities=False,
         perturbed_system=None,
         gcmc=False,
         gcmc_frequency=None,
@@ -363,6 +364,9 @@ def __init__(
             Whether to run replica exchange simulation. Currently this can only be used when
             GPU resources are available.
 
+        randomise_velocities: bool
+            Whether to randomise velocities at the start of each replica exchange cycle.
+
         perturbed_system: str
             The path to a stream file containing a Sire system for the equilibrated perturbed
             end state (lambda = 1). This will be used as the starting conformation all lambda
@@ -539,6 +543,7 @@ def __init__(
         self.opencl_platform_index = opencl_platform_index
         self.oversubscription_factor = oversubscription_factor
         self.replica_exchange = replica_exchange
+        self.randomise_velocities = randomise_velocities
         self.perturbed_system = perturbed_system
         self.gcmc = gcmc
         self.gcmc_frequency = gcmc_frequency
@@ -1645,6 +1650,16 @@ def replica_exchange(self, replica_exchange):
             raise ValueError("'replica_exchange' must be of type 'bool'")
         self._replica_exchange = replica_exchange
 
+    @property
+    def randomise_velocities(self):
+        return self._randomise_velocities
+
+    @randomise_velocities.setter
+    def randomise_velocities(self, randomise_velocities):
+        if not isinstance(randomise_velocities, bool):
+            raise ValueError("'randomise_velocities' must be of type 'bool'")
+        self._randomise_velocities = randomise_velocities
+
     @property
     def perturbed_system(self):
         return self._perturbed_system
diff --git a/src/somd2/runner/_repex.py b/src/somd2/runner/_repex.py
index b0d5663..ae9c7ee 100644
--- a/src/somd2/runner/_repex.py
+++ b/src/somd2/runner/_repex.py
@@ -1240,7 +1240,8 @@ def _run_block(
             _logger.info(f"Running dynamics at {_lam_sym} = {lam:.5f}")
 
             # Draw new velocities from the Maxwell-Boltzmann distribution.
-            dynamics.randomise_velocities()
+            if self._config.randomise_velocities:
+                dynamics.randomise_velocities()
 
             # Run the dynamics.
             dynamics.run(