grompp

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

With annotations covering readOnly, destructive, and idempotency (all false), the description adds that the tool creates a TPR file. However, it does not explain that it may produce warnings, require existing files, or that openWorldHint=true indicates potential side effects beyond the workdir.

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

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

The description is a single 8-word sentence, which is very concise and front-loaded. However, it omits necessary details; a slightly longer description with bullet points would be more helpful while still concise.

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

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

Given 8 parameters (4 required) and no output schema, the description is too minimal. It fails to explain the tool's role in the MD workflow (e.g., that it must precede mdrun), the validation it performs, or that it requires specific input file formats.

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

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

Schema description coverage is 0%, so the description must explain parameters. It only mentions three (MDP, structure, topology) out of eight parameters. Missing explanations for index, maxwarn, workdir, extra_args, and output_tpr, including their defaults and purposes.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb 'Preprocess' and lists inputs (MDP, structure, topology) and output (TPR run input). This distinguishes it from sibling tools like pdb2gmx (which generates structure/topology) and validate_mdp (which only checks inputs).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

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 vs alternatives such as pdb2gmx, solvate, or mdrun. The description does not mention prerequisites, order of operations, 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.