// MCP TOOL REFERENCE

SCICOMP MOLECULAR TOOLS

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

READ TOOLS

analyze_temperature Analyse thermodynamic properties 2/5 detect_phase_transition Identify phase transitions in simulation data 2/5 get_trajectory Retrieve simulation trajectory data 2/5

WRITE TOOLS

add_potential Add Lennard-Jones or Coulomb interaction potentials 3/5 create_particles Initialise a particle system with temperature 3/5

EXECUTE TOOLS

compute_msd Compute mean squared displacement 3/5 compute_rdf Compute radial distribution function 3/5 density_field Compute density field for visualisation 3/5 render_trajectory Animate and render particle trajectories 3/5 run_md Run NVE molecular dynamics simulation 4/5 run_npt Run NPT ensemble simulation (constant pressure) 4/5 run_nvt Run NVT ensemble simulation (constant temperature) 4/5

// 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? +

Use Intercept, the open-source MCP proxy. Write YAML rules for each tool — rate limits, argument validation, or deny rules — then run Intercept in front of the Scicomp Molecular 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.

Enforce policies on Scicomp Molecular

Open source. One binary. Zero dependencies.

npx -y @policylayer/intercept

github.com/policylayer/intercept →