Tutorials

Step-by-step guides for common OHMind workflows, from HEM optimization to multi-step computational chemistry pipelines.

Overview
Prerequisites
Tutorial List
Difficulty Levels
Getting Help
See Also

Overview

These tutorials provide hands-on guidance for using OHMind’s multi-agent system to perform computational chemistry tasks. Each tutorial includes:

Clear objectives - What you’ll accomplish
Step-by-step instructions - Detailed prompts and commands
Expected outputs - What results to expect
Result interpretation - How to understand the outputs
Troubleshooting tips - Common issues and solutions

Prerequisites

Before starting any tutorial, ensure you have:

System Requirements

OHMind installed and configured (Installation Guide)
Conda environment activated (conda activate OHMind)
Workspace directory set up (Workspace Setup)
LLM provider configured (LLM Providers)

For Specific Tutorials

Tutorial	Additional Requirements
HEM Optimization	None (uses built-in models)
QM Calculations	ORCA installed, `OHMind_ORCA` configured
MD Simulations	GROMACS installed and on PATH
Wavefunction Analysis	Multiwfn installed, `MULTIWFN_PATH` configured
Literature Search	Qdrant configured, documents ingested

Starting the Interface

Choose your preferred interface:

Terminal UI (CLI):

cd OHMind
./start_OHMind_cli.sh

Web UI:

cd OHMind
./start_apps.sh
# Open http://localhost:8000

Tutorial List

Beginner Tutorials

Tutorial	Time	Description
HEM Optimization	30 min	Design new cations using PSO optimization
Literature Search	15 min	Search scientific literature with RAG

Intermediate Tutorials

Tutorial	Time	Description
QM Calculations	45 min	Run quantum chemistry calculations with ORCA
MD Simulations	60 min	Perform molecular dynamics with GROMACS

Advanced Tutorials

Tutorial	Time	Description
Multi-Step Workflows	90 min	Combine multiple agents for complex tasks

Difficulty Levels

🟢 Beginner

No external software required (except LLM)
Single-agent workflows
Quick results (< 30 minutes)
Minimal configuration

Recommended starting point: HEM Optimization

🟡 Intermediate

External software required (ORCA, GROMACS)
Single or dual-agent workflows
Moderate computation time
Some configuration needed

Recommended: QM Calculations

🔴 Advanced

Multiple external tools
Multi-agent coordination
Complex workflows
Full system configuration

Recommended: Multi-Step Workflows

Tutorial Workflow

Each tutorial follows this general structure:

graph LR
    A[Setup] --> B[Prompt]
    B --> C[Agent Processing]
    C --> D[Results]
    D --> E[Interpretation]
    E --> F[Next Steps]

1. Setup

Verify prerequisites
Start the interface
Select appropriate chat profile

2. Prompt

Copy the provided prompt
Modify parameters as needed
Submit to the agent

3. Agent Processing

Watch agent activity
Monitor tool calls
Wait for completion

4. Results

Review generated files
Check output locations
Verify completion

5. Interpretation

Understand the results
Compare with expected outputs
Identify key findings

6. Next Steps

Suggested follow-up tasks
Related tutorials
Advanced variations

Quick Start Examples

HEM Optimization (Beginner)

Design new piperidinium-based cations for backbone PBF_BB_1 
optimizing multi-objective HEM performance. Run PSO with 
200 particles for 5 steps.

Expected time: 5-10 minutes
Output: CSV files with top candidates in $OHMind_workspace/HEM/

QM Property Calculation (Intermediate)

For the cation SMILES "C[N+]1(C)CCCCC1", run a QM calculation 
to estimate LUMO energy and alkaline stability descriptors.

Expected time: 10-30 minutes
Output: Optimized geometry and properties in $OHMind_workspace/ORCA/

Literature Search (Beginner)

Search for recent literature on cation designs for hydroxide 
exchange membranes with high alkaline stability. Summarize 
the key structural motifs.

Expected time: 1-2 minutes
Output: Summary with citations

Getting Help

During Tutorials

If you encounter issues:

Check prerequisites - Ensure all requirements are met
Review error messages - Agent responses include diagnostic info
Check workspace - Verify files are being created
Consult troubleshooting - See Troubleshooting Guide

Common Issues

Issue	Solution
“Tool not found”	Check MCP server configuration
“Permission denied”	Verify workspace permissions
“Timeout”	Increase timeout in mcp.json
“Model not found”	Check LLM configuration

Getting Support

Check the Troubleshooting Guide
Review Configuration settings
Consult Agent Reference for capabilities