From e7717ad6e3e3c1d01d3846d64b43c29b0a671271 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Thu, 23 May 2024 14:24:20 +0100
Subject: [PATCH] Need to re-link properties to the reference state since LJ is
 lost.

---
 src/somd2/runner/_runner.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/somd2/runner/_runner.py b/src/somd2/runner/_runner.py
index 40637c4..8adf5a1 100644
--- a/src/somd2/runner/_runner.py
+++ b/src/somd2/runner/_runner.py
@@ -114,6 +114,7 @@ def __init__(self, system, config):
 
             _logger.info("Applying SOMD1 perturbation compatibility.")
             self._system = _make_compatible(self._system)
+            self._system = _morph.link_to_reference(self._system)
 
             # Next, swap the water topology so that it is in AMBER format.