From 88318aa5a416611d3f0679c277e290152b315770 Mon Sep 17 00:00:00 2001
From: hannahbaumann <hbaumann@uci.edu>
Date: Tue, 29 Jul 2025 14:24:58 +0200
Subject: [PATCH] Change the protocol repeat settings to 1

---
 openmm_septop/septop_tutorial.ipynb | 59 +++++++++++++++++++++++------
 1 file changed, 48 insertions(+), 11 deletions(-)

diff --git a/openmm_septop/septop_tutorial.ipynb b/openmm_septop/septop_tutorial.ipynb
index 7d2ef69..97b207b 100644
--- a/openmm_septop/septop_tutorial.ipynb
+++ b/openmm_septop/septop_tutorial.ipynb
@@ -135,7 +135,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Generating charges: 100%|███████████████████████| 10/10 [02:54<00:00, 17.43s/it]\n"
+      "Generating charges: 100%|███████████████████████| 10/10 [02:53<00:00, 17.38s/it]\n"
      ]
     }
    ],
@@ -378,20 +378,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "id": "c2b3de6d-1f11-432d-82f3-9deff16c78dc",
    "metadata": {},
    "outputs": [],
    "source": [
     "from openff.units import unit\n",
     "settings = SepTopProtocol.default_settings()\n",
+    "\n",
+    "# Run only a single repeat\n",
+    "settings.protocol_repeats = 1\n",
+    "# Set the equilibration time to 2 ns (which is also the default)\n",
     "settings.solvent_simulation_settings.equilibration_length = 2000 * unit.picosecond\n",
     "settings.complex_simulation_settings.equilibration_length = 2000 * unit.picosecond"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 14,
    "id": "7adf42d6",
    "metadata": {},
    "outputs": [],
@@ -411,7 +415,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "id": "44ba94ca",
    "metadata": {},
    "outputs": [],
@@ -448,7 +452,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "id": "66666a80",
    "metadata": {},
    "outputs": [],
@@ -493,10 +497,35 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 17,
    "id": "d6cebd9a",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/site-packages/gufe/transformations/transformation.py:124: DeprecationWarning: use of this method is deprecated; instead use `to_json`\n",
+      "  warnings.warn(\n",
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/site-packages/gufe/transformations/transformation.py:124: DeprecationWarning: use of this method is deprecated; instead use `to_json`\n",
+      "  warnings.warn(\n",
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/site-packages/gufe/transformations/transformation.py:124: DeprecationWarning: use of this method is deprecated; instead use `to_json`\n",
+      "  warnings.warn(\n",
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/site-packages/gufe/transformations/transformation.py:124: DeprecationWarning: use of this method is deprecated; instead use `to_json`\n",
+      "  warnings.warn(\n",
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/site-packages/gufe/transformations/transformation.py:124: DeprecationWarning: use of this method is deprecated; instead use `to_json`\n",
+      "  warnings.warn(\n",
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/site-packages/gufe/transformations/transformation.py:124: DeprecationWarning: use of this method is deprecated; instead use `to_json`\n",
+      "  warnings.warn(\n",
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/site-packages/gufe/transformations/transformation.py:124: DeprecationWarning: use of this method is deprecated; instead use `to_json`\n",
+      "  warnings.warn(\n",
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/site-packages/gufe/transformations/transformation.py:124: DeprecationWarning: use of this method is deprecated; instead use `to_json`\n",
+      "  warnings.warn(\n",
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/site-packages/gufe/transformations/transformation.py:124: DeprecationWarning: use of this method is deprecated; instead use `to_json`\n",
+      "  warnings.warn(\n"
+     ]
+    }
+   ],
    "source": [
     "import pathlib\n",
     "# first we create the directory\n",
@@ -510,7 +539,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 18,
    "id": "b96b57a9",
    "metadata": {},
    "outputs": [
@@ -524,6 +553,14 @@
       "rbfe_lig_ejm_31_lig_ejm_48.json rbfe_lig_ejm_46_lig_jmc_28.json\n",
       "rbfe_lig_ejm_31_lig_ejm_50.json\n"
      ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/pty.py:95: DeprecationWarning: This process (pid=12534) is multi-threaded, use of forkpty() may lead to deadlocks in the child.\n",
+      "  pid, fd = os.forkpty()\n"
+     ]
     }
    ],
    "source": [
@@ -569,7 +606,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 19,
    "id": "de7d7920-b171-42fe-9b82-5ff5694d26e5",
    "metadata": {},
    "outputs": [],
@@ -587,7 +624,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 20,
    "id": "0e2e0727-2c4a-4b60-947c-44504aed2eee",
    "metadata": {},
    "outputs": [
@@ -600,7 +637,7 @@
        " 'pint_unit_registry': 'openff_units'}"
       ]
      },
-     "execution_count": 19,
+     "execution_count": 20,
      "metadata": {},
      "output_type": "execute_result"
     }