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Tools · Computational Biology

MD Trajectory Analyzer

Compute RMSD, Rg, RMSF, ligand H-bond occupancy, and representative frames from OpenMM trajectories

Open in the appRun via API

Hardware and price

Price per run

What a typical run reserves from your wallet: the catalog's expected runtime on each piece of hardware × your plan's per-second rate. Larger inputs reserve more, and you're charged only for the seconds the job actually runs.

MD Trajectory Analyzer: reservation per run, USD
HardwareTypical runtimeBasicStarterProEnterprise
CPUDefault30 min$0.25$0.14$0.09$0.054

In workflows

Chain it with other steps.

Each input and output has a data kind, so the builder only connects steps that fit.

Inputs

  • Archive · optionalZIP
  • Protein structure · optionalPDB

Outputs

  • ArchiveZIP
  • StructuresPDB
  • Protein structurePDB
  • TableCSV

References

The method behind it.

  1. Naveen Michaud-Agrawal, Elizabeth J. Denning, Thomas B. Woolf et al. (2011). MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry. doi:10.1002/jcc.21787 (opens in a new tab)
  2. Richard Gowers, Max Linke, Jonathan Barnoud et al. (2016). MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. Proceedings of the Python in Science Conference. doi:10.25080/majora-629e541a-00e (opens in a new tab)

Run via API

Submit it from your own code.

Use an API key from your account. The estimate uses your plan's rates; submitting reserves that amount from your wallet.

# Estimate the reservation for your plan (payload fields: see the API reference)
curl -X POST https://api.cognichem.com/api/v1/jobs/estimate \
  -H "X-Api-Key: $COGNICHEM_API_KEY" \
  -H "Content-Type: application/json" \
  -d '{"job_type": "md-analyze", "resource": "cpu", "payload": {}}'

# Submit (retrying with the same Idempotency-Key never submits twice)
curl -X POST https://api.cognichem.com/api/v1/jobs/submit \
  -H "X-Api-Key: $COGNICHEM_API_KEY" \
  -H "Idempotency-Key: $(uuidgen)" \
  -H "Content-Type: application/json" \
  -d '{"job_name": "md-analyze-1", "job_type": "md-analyze", "resource": "cpu", "payload": { ... }}'
Payload fields and examples in the docs

Computational Biology

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