SepTop: Adapt host min/max distance

Author: hannahbaumann

openmm_septop/septop_tutorial.ipynb

@@ -135,7 +135,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Generating charges: 100%|███████████████████████| 10/10 [02:53<00:00, 17.38s/it]\n"
+      "Generating charges: 100%|███████████████████████| 10/10 [02:54<00:00, 17.43s/it]\n"
      ]
     }
    ],
@@ -378,7 +378,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "id": "c2b3de6d-1f11-432d-82f3-9deff16c78dc",
    "metadata": {},
    "outputs": [],
@@ -388,14 +388,17 @@
     "\n",
     "# Run only a single repeat\n",
     "settings.protocol_repeats = 1\n",
+    "# Change the min and max distance between protein and ligand atoms for Boresch restraints to avoid periodicity issues\n",
+    "settings.complex_restraint_settings.host_min_distance = 0.5 * unit.nanometer\n",
+    "settings.complex_restraint_settings.host_max_distance = 1.5 * unit.nanometer\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": 14,
+   "execution_count": 13,
    "id": "7adf42d6",
    "metadata": {},
    "outputs": [],
@@ -415,7 +418,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 14,
    "id": "44ba94ca",
    "metadata": {},
    "outputs": [],
@@ -452,7 +455,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 15,
    "id": "66666a80",
    "metadata": {},
    "outputs": [],
@@ -497,7 +500,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 16,
    "id": "d6cebd9a",
    "metadata": {},
    "outputs": [
@@ -539,7 +542,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 17,
    "id": "b96b57a9",
    "metadata": {},
    "outputs": [
@@ -558,7 +561,7 @@
      "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",
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/pty.py:95: DeprecationWarning: This process (pid=26930) is multi-threaded, use of forkpty() may lead to deadlocks in the child.\n",
       "  pid, fd = os.forkpty()\n"
      ]
     }
@@ -606,7 +609,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 18,
    "id": "de7d7920-b171-42fe-9b82-5ff5694d26e5",
    "metadata": {},
    "outputs": [],
@@ -624,7 +627,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 19,
    "id": "0e2e0727-2c4a-4b60-947c-44504aed2eee",
    "metadata": {},
    "outputs": [
@@ -637,22 +640,14 @@
        " 'pint_unit_registry': 'openff_units'}"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
     "estimate"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b70822d2-5030-4ed9-87da-f166de551592",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {