Update plain_md.ipynb

OpenFreeEnergy · Mar 6, 2024 · 1ab80eb · 1ab80eb
1 parent 7acd3de
commit 1ab80eb
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/openmm_md/plain_md.ipynb b/openmm_md/plain_md.ipynb
@@ -62,13 +62,13 @@
    "source": [
     "| **Step**                                            | **Software used**                  | **Outputs (with default names)**                           |\n",
     "|:----------------------------------------------------|:-----------------------------------|:-----------------------------------------------------------|\n",
-    "| 1. Input handling using gufe                        | OpenFE, Gufe, RDKit                |\n",
-    "| 2. Parameterization using OpenMMForceFields & OpenFF| OpenFE - OpenMMForceFields - OpenFF| Forcefield cache (`db.json`)\n",
-    "| 3. OpenMM object creation                           | OpenFE - OpenMM + OpenMMTools      | Structure of the full system (`system.pdb`)\n",
-    "| 4. Minimization                                     | OpenFE - OpenMM + OpenMMTools      | Minimized Structure (`minimized.pdb`)\n",
-    "| 5. NVT equilibration (if not gas phase)             | OpenFE - OpenMM + OpenMMTools      | NVT equilibrated structure (`equil_nvt.pdb`)\n",
-    "| 6. NPT equilibration (if not gas phase)             | OpenFE - OpenMM + OpenMMTools      | NPT equilibrated structure (`equil_npt.pdb`)\n",
-    "| 7. NPT production (if not gas phase)                | OpenFE - OpenMM + OpenMMTools      | Simulation trajectory (`simulation.xtc`), Checkpoint file (`checkpoint.chk`), Log output (`simulation.log`)\n"
+    "| 1. Input handling using gufe                        | OpenFE, Gufe, RDKit                ||\n",
+    "| 2. Parameterization using OpenMMForceFields & OpenFF| OpenFE - OpenMMForceFields - OpenFF| Forcefield cache (`db.json`) |\n",
+    "| 3. OpenMM object creation                           | OpenFE - OpenMM + OpenMMTools      | Structure of the full system (`system.pdb`) |\n",
+    "| 4. Minimization                                     | OpenFE - OpenMM + OpenMMTools      | Minimized Structure (`minimized.pdb`) |\n",
+    "| 5. NVT equilibration (if not gas phase)             | OpenFE - OpenMM + OpenMMTools      | NVT equilibrated structure (`equil_nvt.pdb`) |\n",
+    "| 6. NPT equilibration (if not gas phase)             | OpenFE - OpenMM + OpenMMTools      | NPT equilibrated structure (`equil_npt.pdb`) |\n",
+    "| 7. NPT production (if not gas phase)                | OpenFE - OpenMM + OpenMMTools      | Simulation trajectory (`simulation.xtc`), Checkpoint file (`checkpoint.chk`), Log output (`simulation.log`) |\n"
    ]
   },
   {