From 357aa315b15bea8102a4a67f50fa8b9c684477d2 Mon Sep 17 00:00:00 2001
From: PEFrankel <134018002+PEFrankel@users.noreply.github.com>
Date: Wed, 17 Jul 2024 12:35:50 -0600
Subject: [PATCH 1/3] Update _export.py

---
 openff/interchange/interop/gromacs/export/_export.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/openff/interchange/interop/gromacs/export/_export.py b/openff/interchange/interop/gromacs/export/_export.py
index e16f375b..f031d6ca 100644
--- a/openff/interchange/interop/gromacs/export/_export.py
+++ b/openff/interchange/interop/gromacs/export/_export.py
@@ -445,6 +445,7 @@ def _write_gro(self, gro, decimal: int):
         gro.write(f"{n_particles}\n")
 
         count = 0
+        residue_id = 1
         for molecule_name, molecule in self.system.molecule_types.items():
             n_copies = self.system.molecules[molecule_name]
 
@@ -456,7 +457,8 @@ def _write_gro(self, gro, decimal: int):
                         f"%{decimal + 5}.{decimal}f"
                         f"%{decimal + 5}.{decimal}f\n"
                         % (
-                            atom.residue_index,  # This needs to be looked up from a different data structure
+                            residue_id = 1,
+                            # (hidden: 1013) atom.residue_index,  # This needs to be looked up from a different data structure
                             atom.residue_name[:5],
                             atom.name[:5],
                             (count + 1) % 100000,
@@ -467,6 +469,7 @@ def _write_gro(self, gro, decimal: int):
                     )
 
                     count += 1
+                residue_id += 1
 
         if self.system.box is None:
             warnings.warn(

From ce25fc4c600f7de3f68a89419d2857387bcfa1fa Mon Sep 17 00:00:00 2001
From: PEFrankel <134018002+PEFrankel@users.noreply.github.com>
Date: Wed, 17 Jul 2024 12:36:49 -0600
Subject: [PATCH 2/3] Update test_export.py

---
 .../interop/gromacs/export/test_export.py     | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py b/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py
index fbfcaca1..e01d3577 100644
--- a/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py
+++ b/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py
@@ -192,6 +192,27 @@ def test_atom_names_pdb(self):
         openmm_atom_names = openmm.app.GromacsGroFile("atom_names.gro").atomNames
 
         assert openmm_atom_names == pdb_atom_names
+        
+    def test_residue_id_increment(self):
+        """Test that residue IDs increment properly for multiple molecules."""
+
+        mol1 = MoleculeWithConformer.from_smiles("CCO")
+        mol2 = MoleculeWithConformer.from_smiles("CCO")
+
+        for atom in mol1.atoms:
+            atom.metadata["residue_name"] = "MOL1"
+        for atom in mol2.atoms:
+            atom.metadata["residue_name"] = "MOL2"
+
+        interchange = Interchange.from_smirnoff(ForceField("openff-2.0.0.offxml"), [mol1, mol2])
+        interchange.to_gro("resid.gro")
+
+        with open("resid.gro", "r") as gro_file:
+            lines = gro_file.readlines()
+            residue_ids = {int(line[:5].strip()) for line in lines[2:-2]}
+
+            # expecting residue IDs 1 and 2 for MOL1 and MOL2 respectively
+            assert residue_ids == {1, 2}
 
 
 class TestGROMACS(_NeedsGROMACS):

From c39effa366cc7e7a4a0af32b3ed6a54e3372a2ad Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 17 Jul 2024 18:40:13 +0000
Subject: [PATCH 3/3] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .../unit_tests/interop/gromacs/export/test_export.py      | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py b/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py
index e01d3577..dea1935c 100644
--- a/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py
+++ b/openff/interchange/_tests/unit_tests/interop/gromacs/export/test_export.py
@@ -192,7 +192,7 @@ def test_atom_names_pdb(self):
         openmm_atom_names = openmm.app.GromacsGroFile("atom_names.gro").atomNames
 
         assert openmm_atom_names == pdb_atom_names
-        
+
     def test_residue_id_increment(self):
         """Test that residue IDs increment properly for multiple molecules."""
 
@@ -204,10 +204,12 @@ def test_residue_id_increment(self):
         for atom in mol2.atoms:
             atom.metadata["residue_name"] = "MOL2"
 
-        interchange = Interchange.from_smirnoff(ForceField("openff-2.0.0.offxml"), [mol1, mol2])
+        interchange = Interchange.from_smirnoff(
+            ForceField("openff-2.0.0.offxml"), [mol1, mol2]
+        )
         interchange.to_gro("resid.gro")
 
-        with open("resid.gro", "r") as gro_file:
+        with open("resid.gro") as gro_file:
             lines = gro_file.readlines()
             residue_ids = {int(line[:5].strip()) for line in lines[2:-2]}