> ## 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-Bind run > Simulates a protein with a drug-like molecule bound to it, in salt water, to see whether the molecule stays in place, which residues hold it, and optionally how strongly it binds. Each complex 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:** `maxComplexes`: 10. How the engine works and how to read its results: [RevMD-Bind documentation](/docs/revmd-bind). **Scope:** `runs:write`. ## OpenAPI ````yaml /api-reference/openapi.json post /v1/engines/revmd-bind/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-bind/runs: post: tags: - Engine runs summary: Start a RevMD-Bind run description: >- Simulates a protein with a drug-like molecule bound to it, in salt water, to see whether the molecule stays in place, which residues hold it, and optionally how strongly it binds. Each complex 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:** `maxComplexes`: 10. How the engine works and how to read its results: [RevMD-Bind documentation](/docs/revmd-bind). **Scope:** `runs:write`. operationId: engineRuns.revmd-bind 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: 1 ns of a 480-residue protein took about 40 minutes, and its binding energy about 10 more, mostly waiting for a machine. 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 - triclinic edge_distance_nm: default: 1 description: >- Smallest gap, in nm, between the complex 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' 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 binding_energy: default: null description: >- Estimate how strongly the molecule binds, in kcal/mol (MM/PBSA, a fast physics-based approximation), from the saved frames after the simulation. More negative is tighter. null skips it. Not available with CHARMM. anyOf: - type: object properties: methods: default: - gb description: >- How the water around the complex is approximated: gb is faster; pb solves it more exactly and takes longer. Both gives one estimate each. minItems: 1 maxItems: 2 type: array items: type: string enum: - gb - pb per_residue: default: false description: >- Also split the binding energy by protein residue (output binding_energy_by_residue). type: boolean additionalProperties: false - type: 'null' pca: default: false description: >- Also find the complex’s main collective motions (principal component analysis), added as plots. type: boolean advanced: default: vdw_cutoff_nm: 1.2 coulomb_cutoff_nm: 1.2 time_step_ps: 0.002 output_interval_steps: 50000 type: object properties: vdw_cutoff_nm: default: 1.2 description: >- Distance, in nm, beyond which van der Waals forces are ignored. type: number minimum: 0.8 maximum: 2 coulomb_cutoff_nm: default: 1.2 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 output_interval_steps: default: 50000 description: >- Steps between saved frames. Lower gives more frames for the analyses and the binding energy, and larger files. type: integer minimum: 1000 maximum: 100000 additionalProperties: false additionalProperties: false inputs: type: object properties: complexes: type: string description: >- 1 to 10 protein–molecule complexes (the molecule already placed in its pocket, e.g. a docking pose), in PDB or mmCIF format; each is simulated on its own. A file id: an upload (`file_…`) or a Drive file (`dfile_…`, `sdfile_…`). Formats: pdb, cif; up to 50 MB. required: - complexes 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: pose-stability: summary: >- Simulate one docked protein–molecule complex for 1 ns and see which residues hold the molecule. value: name: HSP90 lead pose, 1 ns parameters: {} inputs: complexes: - file_… rank-poses-by-binding-energy: summary: >- Simulate three poses for 5 ns each and estimate each one’s binding energy; compare the children’s totals. value: name: HSP90 top 3 poses, 5 ns + binding energy parameters: simulation_time_ns: 5 binding_energy: methods: - gb inputs: complexes: - file_… - 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.