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gromacs-mcp

gromacs-mcp

by Alierkn
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

write_mdp

Write a safe text MDP or topology file to a work directory, enabling parameter setup for GROMACS simulations.

Instructions

Write a safe text MDP/topology-style file into a work directory.

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": {
      "filename": "<filename>",
      "content": "<content>"
    },
    "name": "write_mdp"
  }
}

Input Schema

NameRequiredDescriptionDefault
contentYes
workdirNo.
filenameYes

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.0

TDQS

C2.3/5.0
Behavior2/5

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

Annotations are provided but are minimal. The description adds 'safe text' but does not explain what 'safe' means (e.g., overwrite behavior, file creation). It lacks details on side effects or authorization needs.

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 a single sentence that is too vague. It omits critical information, making it inefficient for an agent to understand the tool's usage.

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 three parameters, no enums, and low schema coverage, the description is severely incomplete. It does not explain the return value (output schema exists but is not described), nor does it compensate for missing parameter details.

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 input schema has 0% description coverage, and the tool description does not explain any parameters. The purpose of 'content', 'filename', or 'workdir' is not clarified, leaving the agent to guess.

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 states it writes a safe text MDP/topology-style file, which clarifies the tool's purpose and resource type. However, it does not differentiate from sibling tools like write_em_mdp or write_md_mdp, which could lead to confusion.

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?

There is no guidance on when to use this tool versus its siblings, nor any mention of prerequisites, alternatives, or when not to use it.

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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