gromacs-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| GMX_BIN | No | Path to the gmx executable. Default: auto-detected from PATH. | auto |
| GROMACS_MCP_ROOT | No | Base directory for work directories. Default: ~/gromacs-mcp/projects | ~/gromacs-mcp/projects |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| gmx_infoA | Return the GROMACS version, build config, binary path, and project root. |
| list_filesA | List files in a project work directory. |
| read_text_fileB | Read a safe text file from a work directory; output is clipped. |
| write_mdpC | Write a safe text MDP/topology-style file into a work directory. |
| write_em_mdpC | Write a conservative energy-minimisation MDP template. |
| write_nvt_mdpB | Write a conservative NVT equilibration MDP template. |
| write_npt_mdpC | Write a conservative NPT equilibration MDP template. |
| write_md_mdpC | Write a conservative production-MD MDP template. |
| validate_mdpB | Validate a text MDP file for syntax and common safety issues. |
| pdb2gmxC | Build topology and processed coordinates from a PDB/GRO structure. |
| editconfC | Define a simulation box around a structure. |
| solvateC | Fill a box with solvent and update the topology. |
| gromppB | Preprocess MDP, structure, and topology into a TPR run input. |
| genionC | Add counter-ions by replacing solvent molecules. |
| trjconvC | Post-process a trajectory: PBC treatment, centering, and conversion. |
| make_ndxC | Create or edit a GROMACS index file with |
| energyC | Extract an energy term from an EDR file with |
| rmsC | Calculate RMSD with |
| rmsfC | Calculate residue/atom RMSF with |
| gyrateC | Calculate radius of gyration with |
| hbondC | Calculate hydrogen bonds with |
| sasaC | Calculate solvent-accessible surface area with |
| checkC | Check a GROMACS file with |
| mdrun_startB | Start a simulation in the background and return immediately with a job id. |
| mdrun_statusA | Check a background simulation and return progress plus log tail. |
| mdrun_listA | List all known background simulations and their current status. |
| mdrun_stopB | Stop a running background simulation with SIGTERM. |
| mdrun_logsB | Read the captured stdout/stderr log for a background simulation. |
| mdrun_cleanupB | Remove finished job records from the registry. |
| mdrun_forgetA | Remove one job record; running jobs require |
| run_gmxA | Run any non-blocking gmx subcommand not covered by a dedicated tool. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
| prepare_protein_md | Plan a standard solvated-protein MD setup. |
| debug_grompp_failure | Guide debugging of a failed grompp call. |
| basic_trajectory_analysis | Run a basic trajectory analysis set. |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
| projects | List work directories under GROMACS_MCP_ROOT. |
| jobs | List background mdrun jobs. |
TDQS
Scored across 31 tools
Each tool targets a distinct GROMACS operation or file management task. Even the multiple write_mdp tools are clearly differentiated by simulation stage (EM, NVT, NPT, production, generic). The catch-all run_gmx is intentionally generic and does not introduce ambiguity.
Tool names mix several conventions: single-word native GROMACS commands (check, energy), snake_case descriptors (read_text_file, validate_mdp), and a dedicated mdrun_ prefix for job management. While each group is internally consistent, the overall pattern is not uniform, but still readable.
31 tools cover simulation setup, execution, analysis, and file management. This is slightly above average but justified by the breadth of GROMACS. Some generic file operations (list_files, read_text_file) could be omitted, but the count is still reasonable.
Core GROMACS workflows (setup, preprocessing, running, basic analysis) are well covered, but several common analysis tools (e.g., gmx covar, gmx anaeig, gmx distance) and advanced trajectory postprocessing are missing. The surface is functional for typical MD tasks but not exhaustive.