<commit_before>## Pilot 2 Benchmarks for Molecular Dynamics Simulation Data

**Overview**: KRAS MD Simulation Data

### Benchmark Specs Requirements

#### Description of the Data
* Data source: MD Simulation output as PDB files (coarse-grained bead simulation)
* Input dimensions:
** Long term target: ~1.26e6 per time step (6000 lipids x 30 beads per lipid x (position + velocity + type))
** Current: ~288e3 per time step (6000 lipids x 12 beads per lipid x (position + type))
* Output dimensions: 500
* Latent representation dimension:
* Sample size: O(10^6) for simulation requiring O(10^8) time steps
* Notes on data balance and other issues: unlabeled data with rare events

### Sample Data Sets
* RAS
* 3-component-system (DPPC-DOPC-CHOL)
* af-restraints-290k

#### 3K lipids, 10 microseconds simulation, ~3000 frames:
* Disordered - 3k_run10_10us.35fs-DPPC.10-DOPC.70-CHOL.20.dir
* Ordered - 3k_run32_10us.35fs-DPPC.50-DOPC.10-CHOL.40.dir<commit_msg>Fixed a formating error.<commit_after>## Pilot 2 Benchmarks for Molecular Dynamics Simulation Data

**Overview**: KRAS MD Simulation Data

### Benchmark Specs Requirements

#### Description of the Data
* Data source: MD Simulation output as PDB files (coarse-grained bead simulation)
* Input dimensions:
 * Long term target: ~1.26e6 per time step (6000 lipids x 30 beads per lipid x (position + velocity + type))
 * Current: ~288e3 per time step (6000 lipids x 12 beads per lipid x (position + type))
* Output dimensions: 500
* Latent representation dimension:
* Sample size: O(10^6) for simulation requiring O(10^8) time steps
* Notes on data balance and other issues: unlabeled data with rare events

### Sample Data Sets
* RAS
* 3-component-system (DPPC-DOPC-CHOL)
* af-restraints-290k

#### 3K lipids, 10 microseconds simulation, ~3000 frames:
* Disordered - 3k_run10_10us.35fs-DPPC.10-DOPC.70-CHOL.20.dir
* Ordered - 3k_run32_10us.35fs-DPPC.50-DOPC.10-CHOL.40.dir
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