Skip to main content
Glama
Sign In
vmd-hydrate-mcp

vmd-hydrate-mcp

by wjgoarxiv
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

hydrate_order_params

Compute clathrate-hydrate water order parameters F3 and F4 to distinguish hydrate crystals from liquid or ice-Ih in molecular dynamics trajectories.

Instructions

Compute clathrate-hydrate water order parameters F3 (tetrahedrality) and F4 (<cos 3phi>) for a frame. F4 ~ 0.7-0.95 indicates hydrate/crystalline order, ~0 liquid, negative ice-Ih. Units are nm; for .gro the native nm parser is used. This is the differentiating capability no other MCP offers.

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": {
      "path": "<path>"
    },
    "name": "hydrate_order_params"
  }
}

Input Schema

NameRequiredDescriptionDefault
pathYes
frameNo
cutoffNo
topologyNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.0

TDQS

A3.6/5.0
Behavior3/5

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

No annotations are provided, so the description carries full burden. It notes units (nm) and parsing behavior for .gro files, but does not disclose whether the tool is read-only, has side effects, or any performance/rate limits. The agent must infer that it is a computation tool with no state changes.

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

Conciseness4/5

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

The description is concise at two sentences, front-loading purpose and key output interpretation. It could be slightly more structured but is efficient and clear without unnecessary words.

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?

The description lacks details about return values (how F3 and F4 are returned) and parameter descriptions. Despite no output schema, the agent needs to know what the tool returns to use it. The typical F4 range helps but F3 is left undefined, and parameter semantics are missing.

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 must explain parameter meaning. It only mentions 'for a frame' and 'units are nm' but does not describe the four parameters (path, frame, cutoff, topology), their roles, or valid values. The agent lacks key information to set parameters correctly.

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

Purpose5/5

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

The description explicitly states that the tool computes clathrate-hydrate water order parameters F3 (tetrahedrality) and F4 (<cos 3phi>), with typical values provided. It also claims this is the differentiating capability no other MCP offers, clearly distinguishing it from sibling tools like radius_of_gyration or load_structure.

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

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies when to use this tool (when F3/F4 order parameters are needed) by stating it's the only tool offering this capability. However, it does not explicitly mention when not to use it or provide alternatives for related analyses.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

Deploy Server

Other Tools