Bemd

.gitignore

@@ -20,8 +20,12 @@ __pycache__
 *.mp4
 *HBOND_SUMS*
 *HILLS*
+*COLVARS*
 *COLVAR_STD_TORSIONS*
 *COLVAR_REWEIGHT*
 *clustering_output*
 *bespoke-executor*
 *env-bespoke*
+terphenyl_simulations.egg-info/
+*bck.*
+build/

examples/assign_parameters_from_openff/terphenyl_mop/assign_parameters.ipynb

@@ -27,7 +27,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b728de71ea2e475db826e8f7d48a0ac8",
+       "model_id": "b5fae7c03d034f2db2cac7588e83d26a",
        "version_major": 2,
        "version_minor": 0
       },
@@ -58,6 +58,7 @@
    "outputs": [],
    "source": [
     "mol_files = [\n",
+    "    \"../../build_polymer/mop/mop_trimer_mbuild.mol\",\n",
     "    \"../../build_polymer/mop/mop_tetramer_mbuild.mol\",\n",
     "    \"../../build_polymer/mop/mop_hexamer_mbuild.mol\",\n",
     "    \"../../build_polymer/mop/mop_octamer_mbuild.mol\",\n",
@@ -107,11 +108,57 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
+      "mop_trimer_mbuild\n",
       "mop_tetramer_mbuild\n",
-      "mop_hexamer_mbuild\n",
-      "mop_octamer_mbuild\n",
+      "mop_hexamer_mbuild\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/tfobe/Software/openff-toolkit/openff/toolkit/topology/molecule.py:2504: UserWarning: Warning! Partial charge method 'am1bcc' is not designed for use on large (i.e. > 150 atoms) molecules and may crash or take hours to run on this molecule (found 285 atoms). For more, see https://docs.openforcefield.org/projects/toolkit/en/stable/faq.html#parameterizing-my-system-which-contains-a-large-molecule-is-taking-forever-whats-wrong\n",
+      "  warnings.warn(\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'openeye.oequacpac.OEAM1BCCCharges'>\n",
+      "mop_octamer_mbuild\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/tfobe/Software/openff-toolkit/openff/toolkit/topology/molecule.py:2504: UserWarning: Warning! Partial charge method 'am1bcc' is not designed for use on large (i.e. > 150 atoms) molecules and may crash or take hours to run on this molecule (found 373 atoms). For more, see https://docs.openforcefield.org/projects/toolkit/en/stable/faq.html#parameterizing-my-system-which-contains-a-large-molecule-is-taking-forever-whats-wrong\n",
+      "  warnings.warn(\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'openeye.oequacpac.OEAM1BCCCharges'>\n",
       "mop_decamer_mbuild\n"
      ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/tfobe/Software/openff-toolkit/openff/toolkit/topology/molecule.py:2504: UserWarning: Warning! Partial charge method 'am1bcc' is not designed for use on large (i.e. > 150 atoms) molecules and may crash or take hours to run on this molecule (found 461 atoms). For more, see https://docs.openforcefield.org/projects/toolkit/en/stable/faq.html#parameterizing-my-system-which-contains-a-large-molecule-is-taking-forever-whats-wrong\n",
+      "  warnings.warn(\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'openeye.oequacpac.OEAM1BCCCharges'>\n"
+     ]
     }
    ],
    "source": [
@@ -138,7 +185,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "id": "17dbcad7",
    "metadata": {},
    "outputs": [],
@@ -153,16 +200,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "id": "e16c6f45",
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/tfobe/anaconda3/envs/hs_analysis/lib/python3.10/site-packages/openff/interchange/interop/gromacs/export/_export.py:321: UserWarning: WARNING: System defined with no box vectors, which GROMACS does not offically support in versions 2020 or newer (see https://gitlab.com/gromacs/gromacs/-/issues/3526). Setting box vectors to a 5  nm cube.\n",
-      "  warnings.warn(\n"
+      "/home/tfobe/anaconda3/envs/hs_analysis/lib/python3.10/site-packages/openff/interchange/interop/gromacs/export/_export.py:46: UserWarning: WARNING: System defined with no box vectors, which GROMACS does not offically support in versions 2020 or newer (see https://gitlab.com/gromacs/gromacs/-/issues/3526). Setting box vectors to a 5  nm cube.\n",
+      "  self._write_gro(gro, decimal)\n"
      ]
     }
    ],