gromacs-mcp

by Alierkn

Overview Schema Source Related Servers Discussions Admin

Python

Local

editconf

Define a simulation box around a molecular structure. Specify box type, distance, and centering options.

Instructions

Define a simulation box around a structure.

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": "<structure>",
      "workdir": "<workdir>"
    },
    "name": "editconf"
  }
}

Input Schema

Name	Required	Default
`center`	No
`output`	No	box.gro
`workdir`	Yes
`box_type`	No	cubic
`distance`	No
`structure`	Yes
`extra_args`	No

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.2.0Jul 15, 2026

TDQS

C2.6/5.0

Behavior2/5

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

Annotations indicate openWorldHint=true and idempotentHint=false, but the description adds no behavioral context (e.g., whether it modifies the input file or creates a new one). The description does not explain side effects beyond the minimal definition.

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 concise at one sentence, but lacks structure such as usage hints or parameter grouping. It is not overly verbose but could be more informative without added length.

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 7 parameters, 2 required, and an existing output schema, the description is incomplete. It does not explain the tool's role in a simulation pipeline or how the box is defined (e.g., distance from solute).

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?

With 0% schema description coverage, the description fails to explain any of the 7 parameters (e.g., center, distance, box_type). It adds no value beyond the plain parameter names.

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 'Define a simulation box around a structure' clearly states the verb (Define) and resource (simulation box) but does not differentiate from sibling tools like solvate or genion that also modify structures.

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, such as adding a box vs. solvating or adding ions. The description lacks any context cues.

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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