// MCP TOOL REFERENCE

run_md

Run NVE molecular dynamics simulation

Executes compute-intensive simulation

Part of the Scicomp Molecular MCP server. Enforce policies on this tool with Intercept, the open-source MCP proxy.

// WHEN AI AGENTS USE THIS TOOL

AI agents invoke run_md to trigger processes or run actions in Scicomp Molecular. Execute operations can have side effects beyond the immediate call -- triggering builds, sending notifications, or starting workflows. Rate limits and argument validation are essential to prevent runaway execution.

// WHY ENFORCE A POLICY ON RUN_MD

run_md can trigger processes with real-world consequences. An uncontrolled agent might start dozens of builds, send mass notifications, or kick off expensive compute jobs. Intercept enforces rate limits and validates arguments to keep execution within safe bounds.

// RECOMMENDED POLICY

Execute tools trigger processes. Rate-limit and validate arguments to prevent unintended side effects.

io-github-andylbrummer-molecular-mcp.yaml

tools:
  run_md:
    rules:
      - action: allow
        rate_limit:
          max: 10
          window: 60
        validate:
          required_args: true

See the full Scicomp Molecular policy for all 12 tools.

// DETAILS

Tool Name run_md

Category Execute

MCP Server Scicomp Molecular MCP Server

Risk Level High

// MORE SCICOMP MOLECULAR TOOLS

Execute compute_msd Execute compute_rdf Execute density_field Execute render_trajectory Execute run_npt Execute run_nvt Write add_potential Write create_particles

View all 12 tools →

// WHAT CAN GO WRONG

Agents calling execute-class tools like run_md have been implicated in these attack patterns. Read the full case and prevention policy for each:

Browse the full MCP Attack Database →

// OTHER EXECUTE TOOLS ACROSS MCP SERVERS

Other tools in the Execute risk category across the catalogue. The same policy patterns (rate-limit, validate) apply to each.

Agent Passport System — Cryptographic Identity for AI Agents commerce_preflight Agent Passport System — Cryptographic Identity for AI Agents execute_with_context Agent Passport System — Cryptographic Identity for AI Agents gateway_execute_approval Agent Passport System — Cryptographic Identity for AI Agents governance_360 Agent Passport System — Cryptographic Identity for AI Agents parse_governance_block_html AgentClear — API Marketplace for AI Agents call_service

// IN CONTEXT OF HIGH RISK

run_md is one of the high-risk operations in Scicomp Molecular. For the full severity-focused view — only the high-risk tools with their recommended policies — see the breakdown for this server, or browse all high-risk tools across every MCP server.

// RELATED READING

// FAQ

What does the run_md tool do? +

Run NVE molecular dynamics simulation. It is categorised as a Execute tool in the Scicomp Molecular MCP Server, which means it can trigger actions or run processes. Use rate limits and argument validation.

How do I enforce a policy on run_md? +

Add a rule in your Intercept YAML policy under the tools section for run_md. You can allow, deny, rate-limit, or validate arguments. Then run Intercept as a proxy in front of the Scicomp Molecular MCP server.

What risk level is run_md? +

run_md is a Execute tool with high risk. Execute tools should be rate-limited and have argument validation enabled.

Can I rate-limit run_md? +

Yes. Add a rate_limit block to the run_md rule in your Intercept policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block run_md completely? +

Set action: deny in the Intercept policy for run_md. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides run_md? +

run_md is provided by the Scicomp Molecular MCP server (scicomp-molecular-mcp). Intercept sits as a proxy in front of this server to enforce policies before tool calls reach the server.

run_md

Enforce policies on Scicomp Molecular