OHMind-GROMACS MCP Server

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

Table of Contents

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.

Parameters:

Name Type Required Description
smiles string Yes Monomer SMILES
num_chains integer No Number of polymer chains (default: 10)
degree_of_polymerization integer No Chain length (default: 25)
temperature float No Simulation temperature in K (default: 353.15)
water_model string No Water model (default: spce)
simulation_time float No Production time in ns

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.

Parameters:

Name Type Required Description
gro_file string Yes Initial coordinates
top_file string Yes Topology file
temperature float No Target temperature in K
pressure float No Target pressure in bar
production_time float No Production time in ns

Returns: Simulation trajectory and analysis

Estimated Time: 1-4 hours

Analysis Tools

calculate_ions_per_monomer_tool

Calculate ion content from monomer SMILES.

Parameters:

Name Type Required Description
smiles string Yes Monomer SMILES string

Returns: Number of ionizable sites per monomer

analyze_ion_exchange_groups_tool

Advanced analysis of ion-exchange groups in monomers.

Parameters:

Name Type Required Description
smiles string Yes Monomer SMILES string

Returns: Detailed analysis of functional groups

Building Tools

create_polymer_from_smiles_tool

Build oligomer/polymer PDB structures from monomer SMILES.

Parameters:

Name Type Required Description
smiles string Yes Monomer SMILES
degree_of_polymerization integer Yes Number of repeat units
num_chains integer No Number of polymer chains

Returns: Path to generated PDB file

create_itp_file_tool

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

Parameters:

Name Type Required Description
pdb_file string Yes Path to polymer PDB
charge_method string No Charge calculation method

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.

Parameters:

Name Type Required Description
pdb_file string Yes Input PDB file
charge_method string No AM1-BCC or other method

Returns: Parameterization results

prepare_mainchain_files_tool

Produce HEAD/CHAIN/TAIL mainchain definitions.

Parameters:

Name Type Required Description
antechamber_output string Yes Path to Antechamber output

Returns: Mainchain definition files

run_prepgen_tool

Generate PREPI residue files from mainchain definitions.

Parameters:

Name Type Required Description
mainchain_files string Yes Path to mainchain files

Returns: PREPI file path

build_polymer_with_tleap_tool

Build polymer chains with tleap for topology generation.

Parameters:

Name Type Required Description
prepi_file string Yes PREPI residue file
num_chains integer Yes Number of chains
chain_length integer Yes Monomers per chain

Returns: AMBER topology and coordinate files

convert_amber_to_gromacs_tool

Convert AMBER topologies to GROMACS formats.

Parameters:

Name Type Required Description
prmtop string Yes AMBER parameter file
inpcrd string Yes AMBER coordinate file

Returns: GROMACS .top and .gro files

extract_ff_and_itp_tool

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

Parameters:

Name Type Required Description
top_file string Yes GROMACS topology file

Returns: Extracted ITP files

System Preparation Tools

calculate_single_ion_system_tool

Compute system composition and charge balance.

Parameters:

Name Type Required Description
polymer_charge integer Yes Total polymer charge
target_water_content float Yes Water uptake target
ion_type string Yes Counter-ion type

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.

Parameters:

Name Type Required Description
polymer_itp string Yes Polymer ITP file
num_polymers integer Yes Number of polymer chains
num_ions integer Yes Number of counter-ions
water_model string Yes Water model name

Returns: System topology file

create_packmol_input_tool

Run PACKMOL-based initial packing.

Parameters:

Name Type Required Description
components array Yes System components
box_size array Yes Box dimensions

Returns: Packed coordinate file

prepare_simulation_box_tool

Use gmx editconf to define simulation box.

Parameters:

Name Type Required Description
input_gro string Yes Input coordinate file
box_type string No Box type (cubic, dodecahedron)
box_size array No Box dimensions

Returns: Box-defined coordinate file

Simulation Tools

create_mdp_file_tool

Generate MDP files for different simulation phases.

Parameters:

Name Type Required Description
simulation_type string Yes em, nvt, npt, or md
temperature float No Target temperature in K
pressure float No Target pressure in bar
nsteps integer No Number of steps
dt float No Timestep in ps

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.

Parameters:

Name Type Required Description
mdp_file string Yes MDP parameter file
gro_file string Yes Coordinate file
top_file string Yes Topology file

Returns: TPR file path

run_mdrun_tool

⚠️ EXPENSIVE OPERATION - Requires user approval

Execute MD runs with gmx mdrun.

Parameters:

Name Type Required Description
tpr_file string Yes TPR input file
ntomp integer No OpenMP threads

Returns: Trajectory and output files

Analysis Tools

calculate_msd_tool

Compute MSD and diffusion coefficients from trajectories.

Parameters:

Name Type Required Description
trajectory string Yes Trajectory file (.xtc, .trr)
topology string Yes Topology file
selection string Yes Atom selection

Returns: MSD data and diffusion coefficient

analyze_energy_tool

Analyze energies from .edr files.

Parameters:

Name Type Required Description
edr_file string Yes Energy file
terms array Yes Energy terms to extract

Returns: Energy time series and averages

Configuration Tools

get_water_model_info_tool

Get detailed info for a water model.

Parameters:

Name Type Required Description
model_name string Yes Water model name

Returns: Model parameters and usage notes

Available Water Models:

Model Description
spce SPC/E (recommended for IEMs)
tip3p TIP3P
tip4p TIP4P
tip4pew TIP4P/Ew
spc SPC
tip5p TIP5P

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.

Parameters:

Name Type Required Description
new_directory string Yes New work directory path

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:

  1. Check .log file for error messages
  2. Verify topology is correct
  3. Check for overlapping atoms
  4. 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

See Also

Last updated: 2025-12-22 | OHMind v1.0.0

PolyAI Team
Copyright © 2009-2026 Changchun Institute of Applied Chemistry, Chinese Academy of Sciences
Address: No. 5625, Renmin Street, Changchun, Jilin, China. Postal Code: 130022