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Change the protocol repeat settings to 1 #219

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Merged
IAlibay merged 1 commit into from
Jul 30, 2025
Merged

Change the protocol repeat settings to 1 #219

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59 changes: 48 additions & 11 deletions openmm_septop/septop_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
]
}
],
Expand Down Expand Up @@ -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": [],
Expand All @@ -411,7 +415,7 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 15,
"id": "44ba94ca",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -448,7 +452,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 16,
"id": "66666a80",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -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",
Expand All @@ -510,7 +539,7 @@
},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 18,
"id": "b96b57a9",
"metadata": {},
"outputs": [
Expand All @@ -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": [
Expand Down Expand Up @@ -569,7 +606,7 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 19,
"id": "de7d7920-b171-42fe-9b82-5ff5694d26e5",
"metadata": {},
"outputs": [],
Expand All @@ -587,7 +624,7 @@
},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 20,
"id": "0e2e0727-2c4a-4b60-947c-44504aed2eee",
"metadata": {},
"outputs": [
Expand All @@ -600,7 +637,7 @@
" 'pint_unit_registry': 'openff_units'}"
]
},
"execution_count": 19,
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
Expand Down
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