# Stage 2 Medium Researcher-Style Uploaded Trajectory Gate

## Gate result

PASS.

Stage 2 MD Evidence passed a medium researcher-style uploaded trajectory gate.

## Why this gate matters

This gate validates the actual researcher-facing browser upload path with a larger trajectory than the initial small 100-frame upload.

Runtime path:

- browser file picker
- presigned DigitalOcean Spaces upload
- browser-to-Spaces upload
- object verification
- Stage 2 worker job creation through the website
- worker download and hash validation
- topology/trajectory parsing
- RMSD/RMSF/radius-of-gyration descriptive metrics
- persistent result page and artifact downloads

## Job

Job ID:

stage2_20260427_101710_5ps838sa

Result page:

https://protein.neoamorfic.ai/md-evidence/jobs/stage2_20260427_101710_5ps838sa

## Uploaded files

Topology:

researcher_medium_adk_topology.psf

Trajectory:

researcher_medium_adk_trajectory_600_1100.dcd

Metadata:

researcher_medium_adk_metadata.json

## Result summary

Requested files:

3

Completed files:

3

Failed files:

0

Total input bytes:

20877034

Total input size:

19.91 MB

MD metrics computed:

True

Parse status:

parsed

Frame count:

500

Atom count:

3341

Residue count:

214

Selection:

protein

Selection atom count:

3341

Frames analyzed:

500

## Descriptive metrics

### RMSD Angstrom

Mean: 3.747159
Median: 3.674281
Min: 0.0
Max: 8.572133
Std: 1.079108
First: 0.0
Last: 4.792463

### RMSF Angstrom

Mean: 2.511773
Median: 2.040797
Min: 1.065911
Max: 7.881769
Std: 1.331776
First: 1.524594
Last: 2.302316

### Radius of gyration Angstrom

Mean: 19.745699
Median: 19.692964
Min: 17.722191
Max: 21.077071
Std: 0.552105
First: 20.389956
Last: 19.514989

## Gate criteria

completed_files_equal_3:

true

failed_files_equal_0:

true

md_metrics_computed_true:

true

parse_status_parsed:

true

frame_count_500:

true

atom_count_3341:

true

residue_count_214:

true

rmsd_present:

true

rmsf_present:

true

radius_of_gyration_present:

true

STAGE2_MEDIUM_RESEARCHER_STYLE_UPLOAD_PASS:

true

## Claim boundary

This gate validates a researcher-style website upload path and conservative descriptive MD parsing metrics on one medium public trajectory package.

It does not validate:

- biological mechanism
- protein-stability prediction
- binding prediction
- inhibitor analysis
- therapeutic advice
- clinical guidance
- pharma-grade decision support
- replacement for expert MD analysis
- arbitrary large trajectory reliability
- high-concurrency researcher operation