protein-tools-mcp

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rmsd_summary

Analyze GROMACS RMSD .xvg files to detect drift and plateaus, then return an equilibrated or not-equilibrated verdict for simulation equilibration.

Instructions

Assess equilibration from a GROMACS RMSD .xvg file: drift between the first and last 10% of frames, plateau detection, and an equilibrated / not-equilibrated verdict.

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": {
      "xvg_path": "<xvg_path>"
    },
    "name": "rmsd_summary"
  }
}

Input Schema

Name	Required	Description	Default
`xvg_path`	Yes

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

A3.6/5.0

Behavior3/5

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

No annotations exist, so the description carries the full burden. It usefully discloses the exact analysis performed (drift between first/last 10% of frames, plateau detection, binary verdict), but says nothing about error handling for malformed/truncated .xvg files or how the verdict threshold is chosen.

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?

A single front-loaded sentence where every clause carries information: the input type, the three sub-analyses, and the output verdict. No filler.

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

Completeness4/5

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

With an output schema present, return values need not be explained, and the description already previews the verdict concept. For a single-parameter analysis tool this is nearly complete, lacking only sibling routing and failure-mode notes.

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 sole parameter has 0% schema description coverage, but the description compensates by naming the expected input as a GROMACS RMSD .xvg file, which is far more meaningful than the bare 'xvg_path' string type. It still omits path conventions or accepted alternatives.

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?

States a specific verb and resource ('Assess equilibration from a GROMACS RMSD .xvg file') and enumerates the three analyses it performs (drift, plateau detection, verdict). It does not, however, distinguish itself from the sibling xvg_summary, leaving an agent to guess which of the two to pick.

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 implies usage (analyze an RMSD .xvg to judge equilibration) but never states when to use this over xvg_summary, plot_xvg, or rmsf_peaks. No exclusions or prerequisites are given.

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