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Just testing table stuff - please ignore #116

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Merged
hannahbaumann merged 1 commit into from
Mar 7, 2024
Merged

Just testing table stuff - please ignore #116

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14 changes: 7 additions & 7 deletions openmm_md/plain_md.ipynb
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Expand Up @@ -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"
]
},
{
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