OHMind-GROMACS MCP Server

Comprehensive molecular dynamics tools for ion exchange membrane simulations using GROMACS.

Overview
Server Configuration
Tools Reference
Usage Examples
Results Format
Troubleshooting
See Also

Overview

The OHMind-GROMACS MCP server provides 25+ tools for molecular dynamics simulations of polymer ion exchange membranes. It handles the complete workflow from monomer SMILES to production MD and analysis.

Server Details

Property	Value
Server Name	`OHMind-GROMACS`
Entry Point	`python -m OHMind_agent.MCP.GROMACS.server`
Tool Count	25+
Dependencies	GROMACS, AmberTools, PACKMOL, OpenBabel

Capabilities

Polymer building from SMILES
Force field parameterization (AMBER/GAFF)
System preparation and solvation
Ion addition and charge balancing
MD simulation (EM, NVT, NPT, production)
Trajectory and energy analysis
Complete IEM workflow automation

Server Configuration

Starting the Server

# stdio transport (default)
python -m OHMind_agent.MCP.GROMACS.server --transport stdio

# HTTP transport
python -m OHMind_agent.MCP.GROMACS.server --transport streamable-http --port 8105

Environment Variables

Variable	Purpose	Required
`PYTHONPATH`	Path to OHMind project	Yes
`MD_WORK_DIR`	Working directory	Yes
`OHMind_workspace`	Base workspace path	Yes

mcp.json Configuration

{
  "OHMind-GROMACS": {
    "command": "python",
    "args": ["-m", "OHMind_agent.MCP.GROMACS.server", "--transport", "stdio"],
    "env": {
      "PYTHONPATH": "/path/to/OHMind",
      "MD_WORK_DIR": "/OHMind_workspace/GROMACS",
      "OHMind_workspace": "/OHMind_workspace"
    }
  }
}

Software Requirements

Software	Purpose	Required
GROMACS	MD simulations	Yes
AmberTools	Parameterization	Yes
PACKMOL	System packing	Yes
OpenBabel	Format conversion	Recommended

Tools Reference

High-Level Workflow Tools

`run_complete_iem_workflow_tool`

⚠️ VERY EXPENSIVE - Requires user approval

Complete IEM MD workflow from monomer SMILES.

Returns: Complete simulation results

Estimated Time: 1-4 hours

`run_complete_md_simulation_tool`

⚠️ VERY EXPENSIVE - Requires user approval

Full EM → NVT → NPT → MD pipeline.

Returns: Simulation trajectory and analysis

Estimated Time: 1-4 hours

Analysis Tools

`calculate_ions_per_monomer_tool`

Calculate ion content from monomer SMILES.

Returns: Number of ionizable sites per monomer

`analyze_ion_exchange_groups_tool`

Advanced analysis of ion-exchange groups in monomers.

Returns: Detailed analysis of functional groups

Building Tools

`create_polymer_from_smiles_tool`

Build oligomer/polymer PDB structures from monomer SMILES.

Returns: Path to generated PDB file

`create_itp_file_tool`

End-to-end workflow from polymer PDB to GROMACS .itp file.

Returns: Path to generated ITP file

Uses Antechamber + tleap + conversion + extraction pipeline.

Parameterization Tools

`parameterize_molecule_antechamber_tool`

Run Antechamber on a molecule for charges and atom types.

Returns: Parameterization results

`prepare_mainchain_files_tool`

Produce HEAD/CHAIN/TAIL mainchain definitions.

Returns: Mainchain definition files

`run_prepgen_tool`

Generate PREPI residue files from mainchain definitions.

Returns: PREPI file path

`build_polymer_with_tleap_tool`

Build polymer chains with tleap for topology generation.

Returns: AMBER topology and coordinate files

`convert_amber_to_gromacs_tool`

Convert AMBER topologies to GROMACS formats.

Returns: GROMACS .top and .gro files

`extract_ff_and_itp_tool`

Extract forcefield.itp and monomer .itp from a .top file.

Returns: Extracted ITP files

System Preparation Tools

`calculate_single_ion_system_tool`

Compute system composition and charge balance.

Returns: System composition details

Available Ion Types: | Ion | Charge | |—–|——–| | OH | -1 | | Cl | -1 | | Br | -1 | | NO3 | -1 | | ClO4 | -1 | | H2PO4 | -1 | | CO3 | -2 | | SO4 | -2 | | HPO4 | -2 |

`create_system_topology_tool`

Build system .top with polymers, ions, and water.

Returns: System topology file

`create_packmol_input_tool`

Run PACKMOL-based initial packing.

Returns: Packed coordinate file

`prepare_simulation_box_tool`

Use gmx editconf to define simulation box.

Returns: Box-defined coordinate file

Simulation Tools

`create_mdp_file_tool`

Generate MDP files for different simulation phases.

Returns: Path to MDP file

Simulation Types: | Type | Description | |——|————-| | em | Energy minimization | | nvt | NVT equilibration | | npt | NPT equilibration | | md | Production MD |

`run_grompp_tool`

Prepare TPR files via gmx grompp.

Returns: TPR file path

`run_mdrun_tool`

⚠️ EXPENSIVE OPERATION - Requires user approval

Execute MD runs with gmx mdrun.

Returns: Trajectory and output files

Analysis Tools

`calculate_msd_tool`

Compute MSD and diffusion coefficients from trajectories.

Returns: MSD data and diffusion coefficient

`analyze_energy_tool`

Analyze energies from .edr files.

Returns: Energy time series and averages

Configuration Tools

`get_water_model_info_tool`

Get detailed info for a water model.

Returns: Model parameters and usage notes

`list_available_water_models_tool`

List all configured water models.

Returns: Available models with recommendations

`get_current_config_tool`

Report current configuration and work directory.

Returns: Configuration details

`update_work_directory_tool`

Change the default work directory.

Returns: Confirmation

Usage Examples

Small AEM System from SMILES

Using your OHMind-GROMACS tools, start from this monomer SMILES: [SMILES].

1) Estimate ions per monomer and suggest an appropriate ion type and water model.
2) Build an oligomer, parameterize it, generate a real `.itp` file, and create 
   a small system (e.g. 10 chains, DP 25, reasonable water uptake).
3) Run a short MD simulation at 400 K and summarize key properties such as 
   density and qualitatively estimated conductivity.

Focused MD Pipeline Control

I already have `system_initial.pdb` and `system.top`.

Use your GROMACS MCP tools to:
a) Build a simulation box
b) Generate NVT and NPT MDP files with 400 K and 1 bar
c) Run grompp and mdrun for a short production run
d) Analyze MSD and key energy terms

Return a human-readable summary of the MD setup and results.

Water Model Selection

With your configuration tools, list available water models and recommend 
one for hydroxide-conducting AEMs.

Then update the MD work directory to a new folder under my project 
(e.g. `./simulations/aem_test`) and confirm the change.

Temperature Sweep

Using your MD tools, design a small AEM system and run short test 
simulations at 300 K, 350 K, and 400 K.

Compare how water uptake and ionic conductivity change with temperature, 
and provide a brief discussion.

Results Format

Output Directory Structure

MD results are saved to $MD_WORK_DIR/:

$MD_WORK_DIR/
├── system_setup/
│   ├── polymer.pdb
│   ├── polymer.itp
│   └── system.top
├── em/
│   ├── em.mdp
│   ├── em.tpr
│   └── em.gro
├── nvt/
│   ├── nvt.mdp
│   ├── nvt.tpr
│   └── nvt.gro
├── npt/
│   ├── npt.mdp
│   ├── npt.tpr
│   └── npt.gro
├── production/
│   ├── md.mdp
│   ├── md.tpr
│   ├── md.xtc
│   ├── md.edr
│   └── md.gro
└── analysis/
    ├── msd.xvg
    └── energy.xvg

Output File Types

Extension	Contents
`.gro`	GROMACS coordinate file
`.top`	Topology file
`.itp`	Include topology file
`.mdp`	MD parameter file
`.tpr`	Portable binary run input
`.xtc`	Compressed trajectory
`.trr`	Full precision trajectory
`.edr`	Energy file
`.xvg`	XY data (Grace format)

Troubleshooting

Common Issues

GROMACS Not Found

Error: gmx command not found

Solution: Ensure GROMACS is on PATH:

source /path/to/gromacs/bin/GMXRC

AmberTools Not Found

Error: antechamber not found

Solution: Install AmberTools:

conda install -c conda-forge ambertools

PACKMOL Not Found

Error: packmol not found

Solution: Install PACKMOL:

conda install -c conda-forge packmol

Simulation Failed

Error: MD simulation failed

Solutions:

Check .log file for error messages
Verify topology is correct
Check for overlapping atoms
Reduce timestep

Expensive Operations

The following tools require validation:

Tool	Estimated Time
`run_complete_iem_workflow_tool`	1-4 hours
`run_complete_md_simulation_tool`	1-4 hours
`run_mdrun_tool`	Varies

Debug Mode

Run the server with verbose logging:

PYTHONPATH=/path/to/OHMind \
  MD_WORK_DIR=/OHMind_workspace/GROMACS \
  python -m OHMind_agent.MCP.GROMACS.server --transport stdio 2>&1 | tee gromacs_debug.log

OHMind-GROMACS MCP Server

Table of Contents

Overview

Server Details

Capabilities

Server Configuration

Starting the Server

Environment Variables

mcp.json Configuration

Software Requirements

Tools Reference

High-Level Workflow Tools

run_complete_iem_workflow_tool

run_complete_md_simulation_tool

Analysis Tools

calculate_ions_per_monomer_tool

analyze_ion_exchange_groups_tool

Building Tools

create_polymer_from_smiles_tool

create_itp_file_tool

Parameterization Tools

parameterize_molecule_antechamber_tool

prepare_mainchain_files_tool

run_prepgen_tool

build_polymer_with_tleap_tool

convert_amber_to_gromacs_tool

extract_ff_and_itp_tool

System Preparation Tools

calculate_single_ion_system_tool

create_system_topology_tool

create_packmol_input_tool

prepare_simulation_box_tool

Simulation Tools

create_mdp_file_tool

run_grompp_tool

run_mdrun_tool

Analysis Tools

calculate_msd_tool

analyze_energy_tool

Configuration Tools

get_water_model_info_tool

list_available_water_models_tool

get_current_config_tool

update_work_directory_tool

Usage Examples

Small AEM System from SMILES

Focused MD Pipeline Control

Water Model Selection

Temperature Sweep

Results Format

Output Directory Structure

Output File Types

Troubleshooting

Common Issues

GROMACS Not Found

AmberTools Not Found

PACKMOL Not Found

Simulation Failed

Expensive Operations

Debug Mode

See Also

`run_complete_iem_workflow_tool`

`run_complete_md_simulation_tool`

`calculate_ions_per_monomer_tool`

`analyze_ion_exchange_groups_tool`

`create_polymer_from_smiles_tool`

`create_itp_file_tool`

`parameterize_molecule_antechamber_tool`

`prepare_mainchain_files_tool`

`run_prepgen_tool`

`build_polymer_with_tleap_tool`

`convert_amber_to_gromacs_tool`

`extract_ff_and_itp_tool`

`calculate_single_ion_system_tool`

`create_system_topology_tool`

`create_packmol_input_tool`

`prepare_simulation_box_tool`

`create_mdp_file_tool`

`run_grompp_tool`

`run_mdrun_tool`

`calculate_msd_tool`

`analyze_energy_tool`

`get_water_model_info_tool`

`list_available_water_models_tool`

`get_current_config_tool`

`update_work_directory_tool`