Datasets:
Update README.md
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README.md
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@@ -17,20 +17,28 @@ All data in this repository were generated using Density Functional Theory (DFT)
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* System Scale: The dataset covers a wide range of molecular sizes, featuring atomic systems with up to 1,200 atoms, making it uniquely suited for developing scalable models for macromolecular systems.
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### Dataset Components
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The dataset consists of three primary compressed archives, each catering to different aspects of macromolecular force field modeling:
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1. deshaw_protein.tar.gz
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This subset contains protein structures and conformational data extracted from the DE Shaw Research molecular dynamics trajectories [1]. It provides high-fidelity biological samples essential for evaluating the model's ability to generalize across complex protein folding and fluctuation landscapes.
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2. di_molecule_interaction.tar.gz
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This dataset focuses on non-bonded interactions. It was constructed by systematically increasing the distance between two distinct molecules (dimers). It is specifically designed to benchmark long-range interaction modeling, capturing how energy and forces decay as a function of intermolecular separation.
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3. md_traj.tar.gz
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This file contains various molecular dynamics (MD) trajectories generated in-house. It includes a diverse set of chemical systems (e.g., NaCl in water) used to train and validate the model's stability and accuracy in simulating temporal evolution and thermodynamic properties.
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### How-to Load
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The data is stored in **LMDB** format. Using the `md_traj` data as an example, you can load the data as follows:
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* System Scale: The dataset covers a wide range of molecular sizes, featuring atomic systems with up to 1,200 atoms, making it uniquely suited for developing scalable models for macromolecular systems.
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* Data Samples: 677,753.
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### Dataset Components
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The dataset consists of three primary compressed archives, each catering to different aspects of macromolecular force field modeling:
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1. deshaw_protein.tar.gz
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This subset contains protein structures and conformational data extracted from the DE Shaw Research molecular dynamics trajectories [1]. It provides high-fidelity biological samples essential for evaluating the model's ability to generalize across complex protein folding and fluctuation landscapes.
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* Average molecule size: 1065
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* Samples: 42,763
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2. di_molecule_interaction.tar.gz
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This dataset focuses on non-bonded interactions. It was constructed by systematically increasing the distance between two distinct molecules (dimers). It is specifically designed to benchmark long-range interaction modeling, capturing how energy and forces decay as a function of intermolecular separation.
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* Average molecule size: 79
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* Samples: 504,990
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3. md_traj.tar.gz
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This file contains various molecular dynamics (MD) trajectories generated in-house. It includes a diverse set of chemical systems (e.g., NaCl in water) used to train and validate the model's stability and accuracy in simulating temporal evolution and thermodynamic properties.
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* Average molecule size: 525
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* Samples: 130,000
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### How-to Load
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The data is stored in **LMDB** format. Using the `md_traj` data as an example, you can load the data as follows:
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