Merge pull request #422 from openforcefield/dipep-lowe-optimization

Dipeptides lowest energy conformer optimization

README.md

@@ -306,7 +306,7 @@ These are currently used to find a minimum energy conformation of a molecule.
 | `OpenFF NAGL2 Training Optimization Dataset Part 2 v4.0` | [2024-11-19-OpenFF-NAGL2-Training-Optimization-Dataset-Part-2-v4.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-11-19-OpenFF-NAGL2-Training-Optimization-Dataset-Part-2-v4.0) | Optimization dataset for NAGL2 training, part 2 | Si, B, O, I, S, Cl, N, H, C, P, F, Br | |
 | `OpenFF Organometallics Exploratory Optimization Dataset` | [2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset) | Optimization training data for organometallic molecules | F, P, O, C, Zn, N, Ni, Pt, S, Pd, Mg, Br, Rh, Fe, H, Cl, B, Li | |
 | `OpenFF NAGL2 Training Optimization Dataset v4.0` | [2024-12-09-OpenFF-NAGL2-Training-Optimization-Dataset-v4.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-12-09-OpenFF-NAGL2-Training-Optimization-Dataset-v4.0) | Optimization dataset for NAGL2 training, combined and filtered | Si, B, O, I, S, Cl, N, H, C, P, F, Br | |
-
+| `SPICE Dipeptides Lowest E Conformer Optimization Dataset v4.0` | [2025-01-08-SPICE-Dipeptides-Lowest-E-Conformer-Optimization-Dataset-v4.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2025-01-08-SPICE-Dipeptides-Lowest-E-Conformer-Optimization-Dataset-v4.0) | Optimization dataset for the lowest energy conformers of the Dipeptides subset of SPICE | H, S, C, O, N | |
 
 # TorsionDrive Datasets
 These are currently used perform a complete rotation of one or more selected bonds, where optimizations are performed over a discrete set of angles.

submissions/2025-01-08-SPICE-Dipeptides-Lowest-E-Conformer-Optimization-Dataset-v4.0/README.md

@@ -0,0 +1,46 @@
+# SPICE Dipeptides Lowest E Conformer Optimization Dataset v4.0
+
+## Description
+A dataset containing the lowest energy conformer of all molecules from the `Dipeptides` subset of the SPICE dataset, optimized at the OpenFF default level of theory (B3LYP-D3BJ/DZVP). Detailed description on how the original dataset is generated can be found at https://github.com/openmm/spice-dataset/tree/main/dipeptides.
+
+## General information
+* Date: 2025-01-08
+* Class: OpenFF Optimization Dataset
+* Purpose: Conformer optimization
+* Name: SPICE Dipeptides Lowest E Conformer Optimization Dataset v4.0
+* Number of unique molecules: 677
+* Number of conformers: 677
+* Number of conformers (min, mean, max): 1.00, 1.00, 1.00
+* Molecular weight (min, mean, max): 187.20, 313.73, 445.52
+* Charges: -2.0 -1.0 0.0 1.0 2.0
+* Dataset submitter: Alexandra McIsaac
+* Dataset generator: Alexandra McIsaac
+
+## QCSubmit generation pipeline
+* `dipeptide_minEconf.json`: Dataset containing the minimum energy conformers to use as a starting point for the optimization. Needed as an input file to `generate-dataset.ipynb`
+* `generate-dataset.ipynb`: Notebook used to generate dataset
+
+## QCSubmit Manifest
+* `dataset.json.bz2`: Compressed dataset ready for submission
+* `dataset.pdf`: Visualization of dataset molecules
+* `dataset.smi`: Smiles strings for dataset molecules
+* `dipeptide_minEconf.json`: Dataset containing the minimum energy conformers to use as a starting point for the optimization. Needed as an input file to `generate-dataset.ipynb`
+* `generate-dataset.ipynb`: Notebook used to generate dataset
+* `input_environment.yaml`: Environment file used to create Python environment for the notebook
+* `input_environment_full.yaml`: Fully-resolved environment used to execute the notebook.
+
+## Metadata
+* Elements: {H, S, C, O, N}
+* Spec: default-mbis
+  * basis: DZVP
+  * implicit_solvent: None
+  * keywords: {}
+  * maxiter: 200
+  * method: B3LYP-D3BJ
+  * program: psi4
+  * SCF properties:
+    * dipole
+    * quadrupole
+    * mbis_charges
+    * wiberg_lowdin_indices
+    * mayer_indices