MD Agent

Expert agent for molecular dynamics simulations of polymer membranes using GROMACS.

Table of Contents

Overview

The MD Agent specializes in molecular dynamics simulations for ion exchange membranes using GROMACS. It handles system preparation, force field parameterization, simulation execution, and trajectory analysis.

Expertise Areas

  • GROMACS MD simulations
  • Force field parameterization (AMBER/GAFF)
  • System preparation (solvation, ion addition)
  • Polymer building from SMILES
  • Trajectory analysis
  • Transport properties (diffusion, conductivity)

MCP Server

The MD Agent connects to the OHMind-GROMACS MCP server for tool access.

Important Note

Full MD workflows are VERY time-consuming (1-4 hours). The agent will request validation before running expensive simulations.

Capabilities

Capability Description Expensive
Ion Analysis Calculate ions per monomer No
Polymer Building Create polymer from SMILES No
Parameterization Generate force field parameters No
System Setup Prepare simulation box No
Full IEM Workflow Complete membrane simulation ⚠️ Very High
Full MD Simulation EM → NVT → NPT → Production ⚠️ Very High
MSD Analysis Diffusion coefficient calculation No
Energy Analysis Thermodynamic observables No

Available Tools

Analysis Tools

calculate_ions_per_monomer_tool

Calculate ion content from monomer SMILES.

Parameters:

  • smiles (str): Monomer SMILES string

Returns: Number of ionizable sites per monomer

analyze_ion_exchange_groups_tool

Advanced analysis of ion-exchange groups in monomers.

Parameters:

  • smiles (str): 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:

  • smiles (str): Monomer SMILES
  • degree_of_polymerization (int): Number of repeat units
  • num_chains (int): 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:

  • pdb_file (str): Path to polymer PDB
  • charge_method (str): 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:

  • pdb_file (str): Input PDB file
  • charge_method (str): AM1-BCC or other method

Returns: Parameterization results

prepare_mainchain_files_tool

Produce HEAD/CHAIN/TAIL mainchain definitions.

Parameters:

  • antechamber_output (str): Path to Antechamber output

Returns: Mainchain definition files

run_prepgen_tool

Generate PREPI residue files from mainchain definitions.

Parameters:

  • mainchain_files (str): Path to mainchain files

Returns: PREPI file path

build_polymer_with_tleap_tool

Build polymer chains with tleap for topology generation.

Parameters:

  • prepi_file (str): PREPI residue file
  • num_chains (int): Number of chains
  • chain_length (int): Monomers per chain

Returns: AMBER topology and coordinate files

convert_amber_to_gromacs_tool

Convert AMBER topologies to GROMACS formats.

Parameters:

  • prmtop (str): AMBER parameter file
  • inpcrd (str): 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:

  • top_file (str): GROMACS topology file

Returns: Extracted ITP files

System Preparation Tools

calculate_single_ion_system_tool

Compute system composition and charge balance.

Parameters:

  • polymer_charge (int): Total polymer charge
  • target_water_content (float): Water uptake target
  • ion_type (str): Counter-ion type

Returns: System composition details

create_system_topology_tool

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

Parameters:

  • polymer_itp (str): Polymer ITP file
  • num_polymers (int): Number of polymer chains
  • num_ions (int): Number of counter-ions
  • water_model (str): Water model name

Returns: System topology file

create_packmol_input_tool

Run PACKMOL-based initial packing.

Parameters:

  • components (list): System components
  • box_size (list): Box dimensions

Returns: Packed coordinate file

prepare_simulation_box_tool

Use gmx editconf to define simulation box.

Parameters:

  • input_gro (str): Input coordinate file
  • box_type (str): Box type (cubic, dodecahedron)
  • box_size (list): Box dimensions

Returns: Box-defined coordinate file

Simulation Tools

create_mdp_file_tool

Generate MDP files for different simulation phases.

Parameters:

  • simulation_type (str): em, nvt, npt, or md
  • temperature (float): Target temperature in K
  • pressure (float): Target pressure in bar
  • nsteps (int): Number of steps
  • dt (float): Timestep in ps

Returns: Path to MDP file

run_grompp_tool

Prepare TPR files via gmx grompp.

Parameters:

  • mdp_file (str): MDP parameter file
  • gro_file (str): Coordinate file
  • top_file (str): Topology file

Returns: TPR file path

run_mdrun_tool

⚠️ EXPENSIVE OPERATION - Requires user approval

Execute MD runs with gmx mdrun.

Parameters:

  • tpr_file (str): TPR input file
  • ntomp (int): OpenMP threads

Returns: Trajectory and output files

High-Level Workflow Tools

run_complete_iem_workflow_tool

⚠️ VERY EXPENSIVE - Requires user approval

Complete IEM MD workflow from monomer SMILES.

Parameters:

  • smiles (str): Monomer SMILES
  • num_chains (int): Number of polymer chains
  • degree_of_polymerization (int): Chain length
  • temperature (float): Simulation temperature
  • water_model (str): Water model
  • simulation_time (float): 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:

  • gro_file (str): Initial coordinates
  • top_file (str): Topology file
  • temperature (float): Target temperature
  • pressure (float): Target pressure
  • production_time (float): Production time in ns

Returns: Simulation trajectory and analysis

Estimated Time: 1-4 hours

Analysis Tools

calculate_msd_tool

Compute MSD and diffusion coefficients from trajectories.

Parameters:

  • trajectory (str): Trajectory file (.xtc, .trr)
  • topology (str): Topology file
  • selection (str): Atom selection

Returns: MSD data and diffusion coefficient

analyze_energy_tool

Analyze energies from .edr files.

Parameters:

  • edr_file (str): Energy file
  • terms (list): 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:

  • model_name (str): Water model name (SPC/E, TIP3P, etc.)

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.

Parameters:

  • new_directory (str): New work directory path

Returns: Confirmation

Workflow

Complete IEM Simulation Workflow 

graph TD
    A[Monomer SMILES] --> B[calculate_ions_per_monomer]
    B --> C[create_polymer_from_smiles]
    C --> D[create_itp_file]
    D --> E[calculate_single_ion_system]
    E --> F[create_system_topology]
    F --> G[create_packmol_input]
    G --> H[prepare_simulation_box]
    H --> I[Request Approval]
    I --> J[Energy Minimization]
    J --> K[NVT Equilibration]
    K --> L[NPT Equilibration]
    L --> M[Production MD]
    M --> N[calculate_msd]
    N --> O[analyze_energy]
    O --> P[Results Summary]

Example Prompts

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.

Configuration

Environment Variables

Variable Purpose Default
MD_WORK_DIR Working directory $OHMind_workspace/GROMACS
OHMind_workspace Base workspace /OHMind_workspace

Results Storage

MD results are saved to:

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

Expensive Operations

The following tools require validation:

  • run_complete_iem_workflow_tool (1-4 hours)
  • run_complete_md_simulation_tool (1-4 hours)
  • run_mdrun_tool (varies)

See Also

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

PolyAI Team
Copyright © 2009-2025 Changchun Institute of Applied Chemistry, Chinese Academy of Sciences
Address: No. 5625, Renmin Street, Changchun, Jilin, China. Postal Code: 130022