> ## Documentation Index > Fetch the complete documentation index at: https://docs.revilico.bio/llms.txt > Use this file to discover all available pages before exploring further. # Start a RevMD-Aqua run > Simulates how a protein moves in salt water over time (molecular dynamics) and reports how much each residue moves. Each structure is simulated separately, as a child of the run; progress stays at 0 until every child has finished, so follow the child counts. Starts a run and returns it with status `queued`; poll GET /v1/runs/{runId} until it finishes. Runs spend credits. **Limits:** `maxStructures`: 10. How the engine works and how to read its results: [RevMD-Aqua documentation](/docs/revmd-aqua). **Scope:** `runs:write`. ## OpenAPI ````yaml /api-reference/openapi.json post /v1/engines/revmd-aqua/runs openapi: 3.1.0 info: title: Revilico API version: 1.0.0 description: >- Run Revilico's computational chemistry and biology engines from your own code: upload input files, start runs, follow them and read their results. servers: - url: https://public-api.revilico.bio security: - bearerAuth: [] tags: - name: Account description: Who you are, your credits and what your runs have used. - name: Engines description: The engines you can run, their parameter schemas and examples. - name: Files description: 'Upload input files: create an upload, then PUT the bytes.' - name: Runs description: Start, follow and cancel engine runs. - name: Results and outputs description: 'Read what a run produced: results, files and outputs.' - name: Projects description: Group runs into the projects you see in the web app. - name: Sharing description: >- Share runs with people in your organization, as in the web app's Pipeline sharing. - name: Notes description: >- RevNotes: read, write and share the rich-text notes and note folders of the web app's RevNotes panel, in markdown or HTML. - name: Drive description: >- Your RevDrive files and shared drives, as in the web app: browse, read, use files as run inputs, save outputs, and organize. Ids: `dfile_…` and `dfld_…` in a personal Drive, `drive_…` for a shared drive, `sdfile_…` and `sdfld_…` in one. - name: Engine runs description: >- Start a run of one engine, with that engine's parameters and input files. Same endpoint as **Start a run**. - name: Health description: Service status. Needs no API key. paths: /v1/engines/revmd-aqua/runs: post: tags: - Engine runs summary: Start a RevMD-Aqua run description: >- Simulates how a protein moves in salt water over time (molecular dynamics) and reports how much each residue moves. Each structure is simulated separately, as a child of the run; progress stays at 0 until every child has finished, so follow the child counts. Starts a run and returns it with status `queued`; poll GET /v1/runs/{runId} until it finishes. Runs spend credits. **Limits:** `maxStructures`: 10. How the engine works and how to read its results: [RevMD-Aqua documentation](/docs/revmd-aqua). **Scope:** `runs:write`. operationId: engineRuns.revmd-aqua requestBody: required: true content: application/json: schema: type: object properties: name: description: A name for the run, shown in the web app. type: string maxLength: 200 parameters: type: object properties: simulation_time_ns: default: 1 description: >- Length of the simulation, in ns. Run time and cost grow with it: about 13 minutes per ns for a 300-residue protein, plus a few minutes of setup. type: number minimum: 0.1 maximum: 100 force_field: default: amber99sb-ildn description: The set of physics parameters used for the protein. type: string enum: - amber99sb-ildn - amber99sb - amber03 - amber94 - amber96 - amber99 - charmm36-feb2026 water_model: default: tip3p description: >- How water molecules are represented. Must be one the force field ships; tip5p is CHARMM only. type: string enum: - tip3p - tip4p - tip4pew - tip5p - spc - spce box: default: type: cubic edge_distance_nm: 1 type: object properties: type: default: cubic description: >- Shape of the water box. Dodecahedron needs about 30% less water than cubic. type: string enum: - cubic - dodecahedron - octahedral edge_distance_nm: default: 1 description: >- Smallest gap, in nm, between the protein and the box edge. type: number minimum: 0.5 maximum: 3 additionalProperties: false salt: default: type: NaCl concentration_m: 0.15 description: >- Salt added to the water. null adds only the sodium or chloride ions needed to cancel the charge. anyOf: - type: object properties: type: default: NaCl type: string enum: - NaCl - KCl - MgCl2 - CaCl2 - LiCl - RbCl - CsCl - ZnCl2 concentration_m: default: 0.15 description: Salt added, in mol/L. 0.15 is about body fluid. type: number minimum: 0 maximum: 1 additionalProperties: false - type: 'null' ph: default: 7 description: pH used to decide which groups carry a charge. type: number minimum: 0 maximum: 14 temperature_k: default: 300 description: Temperature, in K (300 K is 27 °C). type: number minimum: 250 maximum: 400 pressure_bar: default: 1 description: Pressure, in bar. type: number exclusiveMinimum: 0 maximum: 1000 pca: default: false description: >- Also find the protein’s main collective motions (principal component analysis), added as plots. type: boolean advanced: default: thermostat: V-rescale thermostat_coupling_ps: 0.1 barostat: Parrinello-Rahman barostat_coupling_ps: 2 compressibility_per_bar: 0.000045 vdw_cutoff_nm: 1 coulomb_cutoff_nm: 1 time_step_ps: 0.002 constraints: all-bonds minimization_algorithm: steep max_minimization_steps: 50000 nvt_duration_ps: 100 npt_duration_ps: 100 restraint_force_constant: 1000 temperature_ramp: false pressure_ramp: false output_interval_steps: 15000 type: object properties: thermostat: default: V-rescale description: How the temperature is held steady. type: string enum: - V-rescale - berendsen - nose-hoover thermostat_coupling_ps: default: 0.1 description: >- How quickly the thermostat corrects the temperature, in ps. type: number exclusiveMinimum: 0 maximum: 10 barostat: default: Parrinello-Rahman description: How the pressure is held steady. type: string enum: - Parrinello-Rahman - berendsen barostat_coupling_ps: default: 2 description: >- How quickly the barostat corrects the pressure, in ps. type: number exclusiveMinimum: 0 maximum: 20 compressibility_per_bar: default: 0.000045 description: >- How much the box shrinks per bar of pressure (water: 4.5e-5). type: number exclusiveMinimum: 0 maximum: 0.001 vdw_cutoff_nm: default: 1 description: >- Distance, in nm, beyond which van der Waals forces are ignored. type: number minimum: 0.8 maximum: 2 coulomb_cutoff_nm: default: 1 description: >- Distance, in nm, beyond which charges are handled by the long-range method. type: number minimum: 0.8 maximum: 2 time_step_ps: default: 0.002 description: Length of one simulation step, in ps. type: number minimum: 0.001 maximum: 0.004 constraints: default: all-bonds description: >- Which bond lengths are held fixed, allowing a longer step. type: string enum: - all-bonds - h-bonds - none minimization_algorithm: default: steep description: >- How clashes are removed before the simulation: steepest descent or conjugate gradient. type: string enum: - steep - cg max_minimization_steps: default: 50000 description: Most steps spent removing clashes. type: integer minimum: 1000 maximum: 500000 nvt_duration_ps: default: 100 description: Warm-up at fixed volume, in ps. type: number exclusiveMinimum: 0 maximum: 10000 npt_duration_ps: default: 100 description: Warm-up at fixed pressure, in ps. type: number exclusiveMinimum: 0 maximum: 10000 restraint_force_constant: default: 1000 description: >- How firmly the protein is held in place during warm-up, in kJ/mol/nm². type: number exclusiveMinimum: 0 maximum: 100000 temperature_ramp: default: false description: Raise the temperature gradually during warm-up. type: boolean pressure_ramp: default: false description: Raise the pressure gradually during warm-up. type: boolean output_interval_steps: default: 15000 description: >- Steps between saved frames and energy records. Lower gives more frames and larger files. type: integer minimum: 1000 maximum: 100000 additionalProperties: false additionalProperties: false inputs: type: object properties: structures: type: string description: >- 1 to 10 protein structures in PDB format; each is simulated on its own. Missing atoms are rebuilt and water and other molecules are removed first. A file id: an upload (`file_…`) or a Drive file (`dfile_…`, `sdfile_…`). Formats: pdb; up to 50 MB. required: - structures additionalProperties: false budget: description: Most credits the run may spend; it is stopped beyond that. type: number exclusiveMinimum: 0 projectId: description: >- Add the run to this project (`proj_…`); needs editor or owner on it. type: string required: - inputs additionalProperties: false examples: defaults: summary: >- Simulate one protein for 1 ns in salt water and get how much each residue moves. value: name: KRAS apo 1 ns parameters: {} inputs: structures: - file_… compare-structures: summary: >- Simulate two versions of a protein for 10 ns each in one run; each becomes its own child (child_0, child_1) with its own results. value: name: KRAS wild type vs G12C, 10 ns parameters: simulation_time_ns: 10 box: type: dodecahedron temperature_k: 310 inputs: structures: - file_… - file_… responses: '202': description: OK content: application/json: schema: $ref: '#/components/schemas/Run' '400': $ref: '#/components/responses/400' '401': $ref: '#/components/responses/401' '402': $ref: '#/components/responses/402' '403': $ref: '#/components/responses/403' '404': $ref: '#/components/responses/404' '422': $ref: '#/components/responses/422' '500': $ref: '#/components/responses/500' '502': $ref: '#/components/responses/502' components: schemas: Run: type: object properties: id: type: string description: Run id, `run_…`. engine: type: string description: Engine slug, e.g. `revredox`. name: type: - string - 'null' access: type: string enum: - owner - shared - project description: >- Why you can see the run: you started it, it was shared with you, or it is in a project you belong to. Only the owner can cancel it or read its inputs. owner: type: object properties: name: type: - string - 'null' email: type: string required: - name - email description: Who started the run. status: type: string enum: - queued - running - succeeded - failed - cancelled description: >- queued until the engine picks the run up; succeeded, failed and cancelled are final. statusReason: description: >- Why a cancelled run stopped: `user`, `insufficient_credits` or `budget_exceeded`. Null otherwise. type: - string - 'null' progress: type: number description: Progress the engine reports; 0 until it reports any. createdAt: type: string format: date-time startedAt: anyOf: - type: string format: date-time - type: 'null' endedAt: anyOf: - type: string format: date-time - type: 'null' budget: description: Most credits the run may spend, if one was set. type: - number - 'null' creditsUsed: type: number description: Credits charged to the run so far. error: anyOf: - type: object properties: message: type: string required: - message - type: 'null' description: Set when status is failed. children: type: object properties: total: type: number queued: type: number running: type: number succeeded: type: number failed: type: number cancelled: type: number required: - total - queued - running - succeeded - failed - cancelled description: >- For engines that run each input as its own job: how many children are in each status. GET /v1/runs/{runId}/children lists them. links: type: object propertyNames: type: string additionalProperties: type: string description: >- Related endpoints: self, inputs (owner only), results, outputs, files. warnings: description: >- Set when the run was created but a follow-up step, such as adding it to a project, failed. type: array items: type: string required: - id - engine - name - access - owner - status - statusReason - progress - createdAt - startedAt - endedAt - budget - creditsUsed - error - links Error: type: object properties: error: type: object properties: code: type: string enum: - VALIDATION_FAILED - INVALID_ID - INVALID_PARAMETERS - INPUT_LIMIT_EXCEEDED - NOT_FOUND - FORBIDDEN - METHOD_NOT_ALLOWED - CONFLICT - PAYLOAD_TOO_LARGE - MISSING_CREDENTIALS - INVALID_CREDENTIALS - WRONG_ENVIRONMENT - CREDENTIALS_EXPIRED - CREDENTIALS_REVOKED - ACCOUNT_INACTIVE - API_ACCESS_NOT_ENABLED - INSUFFICIENT_SCOPE - SESSION_REQUIRED - TOO_MANY_AUTH_FAILURES - API_KEY_LIMIT_REACHED - ENGINE_NOT_ENABLED - DOCS_NOT_AVAILABLE - INSUFFICIENT_CREDITS - RUN_NOT_COMPLETE - ENGINE_SUBMIT_FAILED - RATE_LIMITED - SERVICE_UNAVAILABLE - INTERNAL_ERROR description: Stable within /v1; branch on this, not on the message. message: type: string description: Readable explanation, for people. details: description: >- Extra context, e.g. `issues` ({ path, message }[]) for validation errors. type: object propertyNames: type: string additionalProperties: {} required: - code - message required: - error responses: '400': description: >- The request is malformed. `error.code` is one of `VALIDATION_FAILED`, `INVALID_ID`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: VALIDATION_FAILED message: The request is malformed. '401': description: >- The API key is missing or not valid. `error.code` is one of `MISSING_CREDENTIALS`, `INVALID_CREDENTIALS`, `WRONG_ENVIRONMENT`, `CREDENTIALS_EXPIRED`, `CREDENTIALS_REVOKED`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: MISSING_CREDENTIALS message: The API key is missing or not valid. '402': description: >- Your organization doesn't have enough credits. `error.code` is one of `INSUFFICIENT_CREDITS`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INSUFFICIENT_CREDITS message: Your organization doesn't have enough credits. '403': description: >- The key may not do this. `error.code` is one of `INSUFFICIENT_SCOPE`, `API_ACCESS_NOT_ENABLED`, `ENGINE_NOT_ENABLED`, `ACCOUNT_INACTIVE`, `FORBIDDEN`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INSUFFICIENT_SCOPE message: The key may not do this. '404': description: Not found, or not visible to you. `error.code` is one of `NOT_FOUND`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: NOT_FOUND message: Not found, or not visible to you. '422': description: >- The parameters or input files don't fit the engine. `error.code` is one of `INVALID_PARAMETERS`, `INPUT_LIMIT_EXCEEDED`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INVALID_PARAMETERS message: The parameters or input files don't fit the engine. '500': description: >- Something went wrong on our side. `error.code` is one of `INTERNAL_ERROR`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: INTERNAL_ERROR message: Something went wrong on our side. '502': description: >- The engine service rejected or failed the request. `error.code` is one of `ENGINE_SUBMIT_FAILED`. content: application/json: schema: $ref: '#/components/schemas/Error' example: error: code: ENGINE_SUBMIT_FAILED message: The engine service rejected or failed the request. securitySchemes: bearerAuth: type: http scheme: bearer description: >- An API key from the web app (**Settings → Developer**), sent as `Authorization: Bearer rvl_live_…`. ```` This documentation is built and hosted on [Mintlify](https://mintlify.com), a developer documentation platform.