gromacs-mcp

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rms

Computes root-mean-square deviation (RMSD) between trajectory frames and a reference structure to quantify conformational changes.

Instructions

Calculate RMSD with gmx rms.

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": {
      "trajectory": "<trajectory>",
      "tpr": "<tpr>",
      "workdir": "<workdir>"
    },
    "name": "rms"
  }
}

Input Schema

Name	Required	Default
`tpr`	Yes
`output`	No	rmsd.xvg
`workdir`	Yes
`fit_group`	No	Backbone
`extra_args`	No
`trajectory`	Yes
`output_group`	No	Backbone

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.2.0Jul 15, 2026

TDQS

C2.3/5.0

Behavior2/5

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

The description states 'Calculate RMSD' implying a read operation, but annotations include readOnlyHint=false, which is ambiguous but not contradictory. No additional behavioral details are given, such as whether output files are created, or if the tool modifies any state.

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

Conciseness2/5

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

The description is extremely brief (one short sentence), but it is under-specification rather than conciseness. It fails to convey necessary information that could fit in a few more sentences.

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

Completeness1/5

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

Given the tool has 7 parameters (3 required), no schema descriptions, and an output schema, the description is grossly incomplete. It does not mention what RMSD calculates, how to interpret output, or any relationship to other tools.

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

Parameters1/5

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

The description does not provide any meaning or context for the 7 parameters, and the schema has 0% description coverage. For example, 'tpr' and 'trajectory' are critical inputs but their roles are not clarified.

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

Purpose4/5

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

The description clearly states it calculates RMSD using 'gmx rms', which is a specific verb and resource. However, it does not explicitly distinguish from sibling tools like 'rmsf' (RMSF) or 'run_gmx', which might be considered a minor gap.

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

Usage Guidelines2/5

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

No guidance is provided on when to use this tool versus alternatives like 'rmsf' or 'run_gmx'. The description lacks any context about prerequisites, recommended inputs, or typical use cases.

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

Deploy Server

rms