fairchem-mcp

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start_md

Run molecular dynamics (NVT or NVE) in the background with optional step delays for live monitoring between simulation steps.

Instructions

Start molecular dynamics (NVT Langevin or NVE) in the background.

step_delay (seconds) throttles steps so you can observe/react between them.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "structure_id": "<structure_id>",
      "calculator_id": "<calculator_id>"
    },
    "name": "start_md"
  }
}

Input Schema

Name	Required	Default
`structure_id`	Yes
`calculator_id`	Yes
`ensemble`	No	NVT
`temperature_K`	No
`timestep_fs`	No
`steps`	No
`step_delay`	No

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Jun 7, 2026

TDQS

A3.6/5.0

Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden. It discloses that the tool runs 'in the background' and that step_delay throttles steps, giving basic behavioral insight. However, it does not detail side effects, resource usage, blocking behavior, or what happens at the end of the run.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is concise with two sentences, front-loading the core action and immediately providing key detail about step_delay. No redundant or unnecessary information is present.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool has 7 parameters and no output schema or annotations, the description is too brief. It does not explain how to monitor the simulation (e.g., using get_status or get_results), what the return value is, or constraints like units. Important context for a complex simulation tool is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The description adds meaning beyond the schema by explaining step_delay (throttling for observation) and implicitly listing possible ensemble values ('NVT Langevin or NVE'). With 0% schema coverage and 7 parameters, it adds value for two parameters but leaves the rest (structure_id, calculator_id, temperature_K, timestep_fs, steps) without additional context.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb 'start' and the resource 'molecular dynamics', specifying the ensemble types ('NVT Langevin or NVE') and that it runs in the background. This distinguishes it from sibling tools like start_minima_search or start_relaxation, which are different simulation types.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description mentions step_delay to throttle steps for observation, providing some usage context, but lacks explicit guidance on when to use this tool versus alternatives (e.g., other start_* tools) or when to choose NVT vs NVE. It does not include exclusion criteria or prerequisites.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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