// MCP TOOL REFERENCE

SCICOMP MOLECULAR TOOLS

12 tools from the Scicomp Molecular MCP Server, categorised by risk level.

// ALL 12 SCICOMP MOLECULAR TOOLS

READ 3 tools

Read analyze_temperature Analyse thermodynamic properties Read detect_phase_transition Identify phase transitions in simulation data Read get_trajectory Retrieve simulation trajectory data

WRITE 2 tools

Write add_potential Add Lennard-Jones or Coulomb interaction potentials Write create_particles Initialise a particle system with temperature

EXECUTE 7 tools

Execute compute_msd Compute mean squared displacement Execute compute_rdf Compute radial distribution function Execute density_field Compute density field for visualisation Execute render_trajectory Animate and render particle trajectories Execute run_md Run NVE molecular dynamics simulation Execute run_npt Run NPT ensemble simulation (constant pressure) Execute run_nvt Run NVT ensemble simulation (constant temperature)

// RUNNING THIS SERVER

The managed route: connect Scicomp Molecular through the PolicyLayer gateway — every tool call above is checked against your policy before it runs, with a full audit log.

DIRECT INSTALL (UNMANAGED) npx -y scicomp-molecular-mcp

// FAQ

How many tools does the Scicomp Molecular MCP server have? +

The Scicomp Molecular MCP server exposes 12 tools across 3 categories: Read, Write, Execute.

How do I enforce policies on Scicomp Molecular tools? +

Route the Scicomp Molecular server through the PolicyLayer gateway. Define allow, deny, or approval rules per tool in the dashboard — they are enforced on every call before it reaches the server.

What risk categories do Scicomp Molecular tools fall into? +

Scicomp Molecular tools are categorised as Read (3), Write (2), Execute (7). Each category has a recommended default policy.

Let agents act without letting them run wild.

Route your MCP servers through PolicyLayer and every tool call is checked against your policy before it runs — allow, deny, or require approval. Per-identity grants. Full audit log. Live in minutes.

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