diff --git a/openmm_md/plain_md.ipynb b/openmm_md/plain_md.ipynb index 404ba6b..c7f2391 100644 --- 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" ] }, {