{"name":"io.github.wjgoarxiv/vmd-hydrate-mcp","slug":"wjgoarxiv-vmd-hydrate-mcp","title":null,"description":"Drive VMD for GROMACS/LAMMPS analysis + clathrate-hydrate cage science (needs a local VMD)","url":"https://mcp.market/server/wjgoarxiv-vmd-hydrate-mcp","rating":null,"grade":"A","score":88,"certified":false,"status":"active","category":"productivity","tags":["productivity"],"presence":{"score":17,"stars":0,"forks":0,"downloads_week":24,"last_push_at":"2026-07-03T05:34:16.000Z","license":"MIT"},"uptime":null,"claimed":false,"transport":"pypi","callable_via_gateway":false,"default_price_micros":0,"repository":"https://github.com/wjgoarxiv/vmd-hydrate-mcp","website":null,"version":"0.2.0","remotes":[],"packages":[{"registryType":"pypi","identifier":"vmd-hydrate-mcp","version":"0.2.0","transport":{"type":"stdio"}}],"tools":[{"name":"add_representation","description":"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.","write_action":false,"price_micros":0,"input_schema":null},{"name":"clear_representations","description":"Remove all representations from a molecule (start a fresh view).","write_action":true,"price_micros":0,"input_schema":null},{"name":"hbond_network","description":"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).","write_action":false,"price_micros":0,"input_schema":null},{"name":"hydrate_order_params","description":"Compute clathrate-hydrate water order parameters F3 (tetrahedrality) and F4 (<cos 3phi>) for a frame. 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