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gromacs-mcp

gromacs-mcp

by Alierkn
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

energy

Extracts a specified energy term from a GROMACS energy file (EDR) using the gmx energy command. Accepts options for selection and output file.

Instructions

Extract an energy term from an EDR file with gmx energy.

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": {
      "energy_file": "<energy_file>",
      "workdir": "<workdir>"
    },
    "name": "energy"
  }
}

Input Schema

NameRequiredDescriptionDefault
outputNoenergy.xvg
workdirYes
selectionNoPotential
extra_argsNo
energy_fileYes

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.0

TDQS

C2.8/5.0
Behavior2/5

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

The description says 'extract', implying a read-only operation, but annotations set readOnlyHint=false, which is contradictory. No other behavioral details are provided (e.g., file creation, permissions). The description does not clarify the discrepancy.

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

Conciseness4/5

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

The description is a single sentence, making it very concise. However, it could include more useful information without becoming overly long.

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 no parameter descriptions in the schema, five parameters, and minimal behavioral context, the description is insufficient. It does not cover how to specify the energy term or output file, nor does it explain the tool's role among many siblings.

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?

With 0% schema description coverage, the description bears full responsibility for parameter meaning. However, it mentions none of the five parameters (output, workdir, selection, extra_args, energy_file), leaving them completely unexplained.

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 tool extracts an energy term from an EDR file using the gmx energy command. It specifies the resource (EDR file) and the operation (extract), which distinguishes it from siblings like rms or rmsf.

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?

The description provides no guidance on when to use this tool versus alternatives (e.g., which energy terms are available, or when to use other tools). It only states the generic action, leaving the agent to infer usage context.

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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