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gromacs-mcp

gromacs-mcp

by Alierkn
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

check

Validate GROMACS files for errors to ensure correct molecular dynamics simulations. Detects issues in structure and topology files.

Instructions

Check a GROMACS file with gmx check.

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": {
      "input_file": "<input_file>",
      "workdir": "<workdir>"
    },
    "name": "check"
  }
}

Input Schema

NameRequiredDescriptionDefault
workdirYes
extra_argsNo
input_fileYes

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.0

TDQS

C2.4/5.0
Behavior1/5

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

The description describes a read-only operation ('Check a GROMACS file'), but the annotation readOnlyHint is false, creating a contradiction. The description does not disclose any other behavioral traits beyond the annotations, which are themselves inconsistent.

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

Conciseness3/5

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

The description is a single sentence with no wasted words, but it is too brief to convey necessary information. It earns its place but misses significant context.

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 3 parameters, many siblings, and an output schema, the description is incomplete. It does not explain what the tool returns, how parameters affect behavior, or how it differs from similar tools.

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

Parameters2/5

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

Schema description coverage is 0% and the description adds no meaningful information about any of the 3 parameters (workdir, extra_args, input_file). Only the input_file parameter is loosely implied by 'GROMACS file', but no details are given.

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 specifies the verb 'Check' and the resource 'GROMACS file', and ties it to the specific command 'gmx check'. It is clear but does not elaborate on the nature of the check (e.g., validation, integrity), and does not differentiate it from sibling tools like gmx_info or read_text_file.

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. There is no mention of scenarios, prerequisites, or exclusions. The usage context is only implied from the tool name and command reference.

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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