Gromacs MCP Server
gromacs-mcp
PyPI
v0.2.0
Published by alierkn — no publish provenance, so origin is unverified, but the source is public: the repository link below is self-declared yet readable, so you can inspect the code before adopting it.
Model Context Protocol server that drives a local GROMACS installation — build, solvate, ionize, run simulations in the background, and analyse trajectories from any MCP client.
The grade answers one question — how safe is this server for you to adopt — so it is computed in two auditable stages. Nothing below is an opinion or an LLM's guess; every line is a real term the deterministic engine applied, and the same input always yields the same number.
1. Threat score — 100 − 0 = 100. What the published surface and source actually contain:
The deterministic scan raised no scored threat in the surface it inspected — the threat score stayed at 100. Capability observations and advisory notes are recorded but never lower it.
2. Client adoption risk — 100 − 7 = 93. Three small, subtract-only factors that reflect your risk in adopting it — a clean scan proves less on a powerful, unverified or barely-inspectable package, so the grade says so plainly:
| Points | Adoption-risk factor |
|---|---|
| −6 | capability blast radius (high) — client exposure if the model is manipulated |
| −1 | publisher verification (public source) — no provenance, but the source is public and inspectable |
Capability observations and info notes are shown under Findings but never scored.
Open any row's finding below for the file, line and evidence behind a deduction.
Findings 2
high Reads a sensitive credential path or dumps the environment (src/gromacs_mcp/server.py)MTC-SRC-006
In the server's implementation (`src/gromacs_mcp/server.py:121`): Reading private keys / cloud credentials, or serializing the whole environment, is a sensitive-data source that becomes exfiltration when combined with any egress. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.
Evidence: , ".env.local", ".netrc", "authorized_keys", "id_dsa", "id_ecdsa", "id_ed25519", "id_rsa",
Fix: Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.
Location: server src/gromacs_mcp/server.py
high Shell/command execution in server code (src/gromacs_mcp/server.py)MTC-SRC-002
In the server's implementation (`src/gromacs_mcp/server.py:355`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.
Evidence: try: proc = subprocess.run( cmd, cwd=str(workdir), input=stdin,
Fix: Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.
Location: server src/gromacs_mcp/server.py
Tools 31
Each tool and what it can reach — statically extracted from the published source.
list_filesreads sensitive datacheckno sensitive capabilityeditconfno sensitive capabilityenergyno sensitive capabilitygenionno sensitive capabilitygmx_infono sensitive capabilitygromppno sensitive capabilitygyrateno sensitive capabilityhbondno sensitive capabilitymake_ndxno sensitive capability
Show 21 more tools ↓
mdrun_cleanupno sensitive capabilitymdrun_forgetno sensitive capabilitymdrun_listno sensitive capabilitymdrun_logsno sensitive capabilitymdrun_startno sensitive capabilitymdrun_statusno sensitive capabilitymdrun_stopno sensitive capabilitypdb2gmxno sensitive capabilityread_text_fileno sensitive capabilityrmsno sensitive capabilityrmsfno sensitive capabilityrun_gmxno sensitive capabilitysasano sensitive capabilitysolvateno sensitive capabilitytrjconvno sensitive capabilityvalidate_mdpno sensitive capabilitywrite_em_mdpno sensitive capabilitywrite_md_mdpno sensitive capabilitywrite_mdpno sensitive capabilitywrite_npt_mdpno sensitive capabilitywrite_nvt_mdpno sensitive capability
What this scan could not see
- Tools were statically extracted from the published source (31 recovered), not enumerated from a running server. Tool-poisoning, Unicode-smuggling, capability and toxic-flow analysis ran on this inferred surface, but a mis-parsed registration could be missed or mis-attributed, so tool-derived findings are capped below “confirmed”. To grade the real runtime surface, scan the running server: --command "npx -y <package>".
Versions 1
Scan history per published version. The engine is deterministic — the same version always yields the same score, so a changed score means the package itself changed.
| Version | Score | Findings | Engine | Scanned |
|---|---|---|---|---|
v0.2.0 latest |
A 93/100 | 2 | 1.13.0 | 2026-08-25 |
Embed this score
Show this server's live Trust Score in your README, docs or website. The badge is served straight from the registry and updates automatically after every rescan — no API key needed. It links back to this page, so anyone who sees the grade can also read the findings behind it instead of taking a number on faith.
Verify this score yourself
The score above is reproducible: the same package version always yields the same result. Run it locally or over the free API — no account, no LLM, fully deterministic.
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