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Alierkn
by Alierkn

rmsf

Calculate residue or atom root mean square fluctuation from a trajectory and topology file.

Instructions

Calculate residue/atom RMSF with gmx rmsf.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
tprYes
groupNoProtein
outputNormsf.xvg
workdirYes
extra_argsNo
trajectoryYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior2/5

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

Annotations indicate limited behavioral traits (not read-only, not destructive). The description adds no additional behavioral context, such as side effects, system changes, or required permissions. It does not contradict annotations.

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 very short (one sentence) and gets to the point, which is acceptable for a simple tool. However, it could include a bit more detail without becoming verbose.

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 6 parameters (3 required) and an output schema, the description is severely incomplete. It fails to explain what RMSF is, the meaning of key parameters, or the expected output format.

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 description provides no information about any of the six parameters, despite 0% schema description coverage. It does not explain the role of 'group', 'output', 'extra_args', etc.

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 clearly states the action 'Calculate' and the resource 'residue/atom RMSF' with the underlying command 'gmx rmsf'. However, it does not differentiate from sibling tools like 'rms' or 'energy', which is a minor gap.

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, nor any prerequisites, limitations, or when not to use it. The description is purely functional with no 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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