Skip to main content
All tools

Tools · Computational Biology

OpenMM MD

Prepare, solvate, and equilibrate protein structures with OpenMM molecular dynamics

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.

OpenMM MD: reservation per run, USD
HardwareTypical runtimeBasicStarterProEnterprise
CPU1 h$0.50$0.29$0.18$0.11
Nvidia T4Default2 h$4.10$2.95$2.38$1.80
Nvidia L42 h$5.62$4.03$3.17$2.38
Nvidia A102 h$7.70$5.47$4.39$3.31
Nvidia L40S2 h$13.68$9.79$7.78$5.83
Nvidia A100, 40 GB2 h$14.69$10.51$8.42$6.34
Nvidia A100, 80 GB2 h$17.50$12.53$10.01$7.49
Nvidia H1002 h$27.65$19.73$15.77$11.88
Nvidia H2002 h$31.75$22.68$18.14$13.61
Nvidia B2002 h$43.78$31.25$24.98$18.79

In workflows

Chain it with other steps.

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

Inputs

  • Molecules · optionalSMILES
  • Protein structurePDB

Outputs

  • ArchiveZIP
  • Protein structurePDB

References

The method behind it.

  1. Peter Eastman, Raimondas Galvelis, Raúl P. Peláez et al. (2023). OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The Journal of Physical Chemistry B. doi:10.1021/acs.jpcb.3c06662 (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": "openmm-md", "resource": "t4", "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": "openmm-md-1", "job_type": "openmm-md", "resource": "t4", "payload": { ... }}'
Payload fields and examples in the docs

Computational Biology

Related tools

  • Boltz-2

    Accurate in silico screening for early-stage drug discovery

  • BoltzGen

    Design proteins and peptides to bind biomolecular targets

  • DiffDock

    Protein-ligand docking with diffusion models and confidence-ranked poses

  • DrugFlow

    Generate candidate ligands from a protein target and reference ligand using flow matching

  • Sequence Mutator

    Apply point mutations such as T315I to a protein sequence, checking each wild-type residue

  • ESMFold2

    Predict protein, DNA, RNA, and ligand complex structures with evolutionary scale modeling

All tools