Vmd Hydrate MCP server

Read from the package source without running it. The installed server may list more.

• add_representation

  Add a representation WITHOUT clearing existing ones — layer several reps (e.g. water as Points + solute as VDW). `color` is a coloring METHOD (Name, ResName, ResType, Chain, Beta, ...); `style` is VDW/Lines/Points/ NewCartoon/Licorice/etc.

• clear_representationswrite action

  Remove all representations from a molecule (start a fresh view).

• hbond_network

  Build the water-water hydrogen-bond network for a frame and report bond count and average coordination (the substrate for cage identification). rcut is the O-O cutoff (nm), theta the H-O...O angle cutoff (degrees).

• hydrate_order_paramswrite action

  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.

• identify_cages

  Identify clathrate-hydrate cages (5^12, 5^12 6^2, 5^12 6^4, ...) from the water H-bond network and classify the crystal structure (sI/sII/sH). Returns per-type cage counts, the structure label, and a confidence. method="TRACE" (all rings) or "HTR" (primitive rings). GROMACS .gro input.

• list_molecules

  List molecules currently loaded in the VMD session (molid, path, atoms, frames).

• load_structure

  Load a structure/trajectory into the persistent VMD session for visualization. Supports PDB, GROMACS (.gro/.xtc/.trr), LAMMPS (.data/dump), DCD. Coordinate-only formats (.xtc/.trr/.dcd) require a `topology`. Returns the molid used to reference this molecule in later calls.

• measure_geometry

  Measure a distance (2 atom indices), angle (3), or dihedral (4) at a frame. Distances are in Angstrom, angles in degrees.

• radius_of_gyration

  Radius of gyration (Angstrom) of an atom selection at a frame.

• render

  Render the current view of a loaded molecule headlessly (CPU Tachyon) and return a PNG image. Resolution is capped for safety.

• render_cages

  Render clathrate cages photorealistically (ambient occlusion + shadows, orthographic by default). Each cage type is drawn in ONE unified color for both its water-oxygen vertices and its O-O framework, using a curated palette (512=cyan, 51262=violet, 51264=red, 435663=lime, 51268=blue).

• reset_view

  Reset/fit the camera to the loaded molecule.

• resolve_selection

  Report how many atoms an MDAnalysis selection matches — use this to catch the common 0-atom trap on bare .gro files before running measurements.

• rotate_view

  Rotate the camera by `degrees` about an axis ('x'/'y'/'z'). In GUI/attended mode (VMD_HYDRATE_MCP_DISPLAY=gui) the visible window updates live.

• set_representation

  Set the visual representation of a loaded molecule (e.g. style=NewCartoon, Licorice, VDW, Lines; color=Name, ResType, Beta; selection is a VMD atom-selection string like "water" or "name CA").

• vmd_status

  Report whether VMD is available, its version, and the molecules currently loaded in the persistent session.

• zoom_view

  Zoom the view by a multiplicative factor (>1 zoom in, <1 zoom out).

• Code scan22 source files scanned25/25
• –Live reliabilityno gateway calls yet and no remote to proben/a
• –Tool poisoningtools not inspected (local package is not executed); not countedn/a
• Auth qualitylocal package, no credentials required12/15
• Maintenancelast push 85 days ago12/15
• Maintainer identityregistry namespace matches repository owner; GitHub account older than a year8/10

Safety score

88/100

higher than 75% of 1,299 Productivity servers

Tools

17

the typical Productivity server has 7

Tools that change things

12%

typical: 0%. Fewer write tools means less an agent can break

Downloads a week

24

more than 9% of 427 Productivity servers with a package

Vmd Hydrate: common questions

Is Vmd Hydrate MCP server safe?

Yes, by our scan: it is graded A (88/100). Read the Vmd Hydrate safety report

How do I install Vmd Hydrate?

It runs on your machine. Copy the Claude Code, Cursor, VS Code or Claude Desktop config from the install section.

Does Vmd Hydrate need an API key?

Not as far as the registry entry and our scan can tell: no credentials are declared or required.

Is Vmd Hydrate maintained?

The last commit was 124 days ago (2026-07-03). The latest release is v0.2.0.

What can I use instead of Vmd Hydrate?

Servers from other publishers that do the same job: Argent MCP server, gflow-cli MCP server and Buoy Gg MCP server.

How does Vmd Hydrate compare with other Productivity MCP servers?

safety score 88/100 (higher than 75% of 1,299 Productivity servers); tools 17 (the typical Productivity server has 7); tools that change things 12% (typical: 0%. Fewer write tools means less an agent can break). Full comparison.