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Computational Chemistry LaTeX Template for CoCalc

A comprehensive, SEO-optimized LaTeX template for computational chemistry research featuring molecular dynamics simulations, quantum chemistry calculations, and drug discovery applications. Designed specifically for CoCalc with embedded PythonTeX calculations and reproducible workflows.

Keywords & Search Terms

Primary Keywords:

  • computational chemistry latex template

  • molecular dynamics latex

  • quantum chemistry template

  • DFT calculations latex

Secondary Keywords:

  • protein structure latex

  • drug discovery latex template

  • molecular visualization latex

  • gaussian output latex template

Long-tail Keywords:

  • pymol figures latex

  • rdkit chemistry latex

  • amber molecular dynamics latex

  • homo lumo latex template

  • reaction pathway latex

  • solvation energy latex

Features

🧬 Molecular Systems & Visualization

  • 3D molecular structure representations

  • HOMO/LUMO orbital visualizations

  • Electron density plots and energy surfaces

  • Protein-ligand interaction analysis

  • Chemical reaction mechanisms and pathways

⚛️ Quantum Chemistry Applications

  • DFT energy calculations and property prediction

  • Vibrational frequency analysis

  • Transition state searches and IRC calculations

  • Natural bond orbital (NBO) analysis

  • Basis set convergence studies

🧪 Molecular Dynamics Simulations

  • RMSD/RMSF trajectory analysis

  • Temperature and pressure monitoring

  • Solvation shell and radial distribution functions

  • Protein conformational dynamics

  • Ligand binding free energy calculations

💊 Drug Discovery & Design

  • Virtual screening result analysis

  • Molecular docking scores and poses

  • ADMET properties prediction

  • Structure-activity relationships (SAR)

  • Pharmacophore modeling and optimization

📊 Data Visualization & Analysis

  • Publication-quality matplotlib figures

  • Interactive molecular plots

  • Energy landscape visualization

  • Statistical analysis of simulation data

  • Comparative studies and benchmarking

Quick Start

Prerequisites

Ensure you have the following packages installed in CoCalc:

  • Python 3 with numpy, matplotlib, scipy, seaborn

  • LaTeX with pythontex, chemfig, mhchem packages

  • Shell escape enabled for code execution

Compilation Instructions

# Build the complete template
make all

# Quick compilation without PythonTeX
make quick

# Clean auxiliary files
make clean

# Force complete rebuild
make rebuild

# Test compilation
make test

Method 2: Using latexmk

# Automatic compilation with PythonTeX
latexmk -pdf -shell-escape main.tex

# Clean build files
latexmk -c

Method 3: Manual Compilation

# Step-by-step compilation for troubleshooting
pdflatex -shell-escape main.tex
pythontex main.tex
pdflatex -shell-escape main.tex
pdflatex -shell-escape main.tex

Template Structure

computational-chemistry/
├── main.tex              # Main template file with embedded Python
├── Makefile              # Build automation
├── latexmkrc             # LaTeX compilation configuration
├── README.md             # This documentation
├── metadata.json         # Template metadata
├── LICENSE               # MIT license
├── assets/               # Generated figures and molecular structures
│   ├── homo_lumo_gaps.pdf
│   ├── md_analysis.pdf
│   ├── virtual_screening.pdf
│   ├── protein_ligand_interactions.pdf
│   ├── reaction_pathway.pdf
│   └── molecular_orbitals.pdf
├── code/                 # Optional analysis scripts
└── build/                # Temporary build files

CoCalc-Specific Features

TimeTravel Integration

  • Create checkpoints after successful builds

  • Track template evolution and modifications

  • Collaborate with version control

AI Assistant Integration

Use these prompts with CoCalc's AI assistant:

  • "Help me modify the DFT calculation parameters"

  • "Suggest improvements for the molecular visualization"

  • "Optimize the drug discovery analysis section"

  • "Add additional quantum chemistry methods"

Collaboration Features

  • Real-time collaborative editing

  • Shared project workspace

  • Comment and suggestion system

  • Live preview of compilation results

Terminal Integration

Open a terminal in CoCalc and use:

# Install additional chemistry packages
pip install --user rdkit-pypi MDAnalysis

# Monitor compilation progress
make all 2>&1 | tee build.log

# Generate molecular structures
python code/generate_structures.py

Customization Guide

Adding New Calculations

  1. Insert new pycode blocks in the LaTeX document

  2. Use matplotlib for publication-quality figures

  3. Save results to the assets/ directory

  4. Reference figures with \includegraphics{assets/filename.pdf}

Modifying Molecular Systems

  • Update coordinate data in Python code blocks

  • Adjust force field parameters for MD simulations

  • Modify basis sets and DFT functionals

  • Change molecular visualization styles

Extending Analysis

  • Add new statistical analysis methods

  • Include machine learning predictions

  • Integrate with external computational chemistry tools

  • Implement custom plotting functions

Troubleshooting

Common Issues

PythonTeX not found:

# Install PythonTeX
pip install --user pythontex

Shell escape disabled:

  • Ensure -shell-escape flag is used in compilation

  • Check CoCalc project settings for code execution

Missing Python packages:

# Install required packages
make install-deps

Figure generation errors:

  • Check assets/ directory permissions

  • Verify matplotlib backend configuration

  • Review Python code for syntax errors

Build Errors

  1. LaTeX compilation fails:

    • Check for package conflicts

    • Verify all required packages are installed

    • Review error messages in build log

  2. Python code execution errors:

    • Test Python code blocks independently

    • Check import statements and dependencies

    • Verify data file paths and accessibility

  3. Figure display issues:

    • Ensure PDF figures are generated correctly

    • Check includegraphics paths

    • Verify figure file permissions

Performance Optimization

For Large Calculations

  • Use run_in_background for long computations

  • Implement caching for expensive calculations

  • Split large datasets into smaller chunks

  • Utilize CoCalc's computational resources efficiently

For Collaboration

  • Use .tasks files for distributed calculations

  • Implement progress tracking for long simulations

  • Cache intermediate results for team sharing

  • Document calculation parameters clearly

Citation & Licensing

This template is released under the MIT License. When using this template in publications, please cite:

@misc{cocalc_compuchem_template,
  title={Computational Chemistry LaTeX Template for CoCalc},
  author={CoCalc Scientific Templates},
  year={2024},
  url={https://github.com/cocalc-scientific-templates/computational-chemistry},
  note={Molecular dynamics, quantum chemistry, and drug discovery applications}
}

  • Quantum Chemistry Calculations: Focus on DFT and ab initio methods

  • Molecular Dynamics Analysis: Specialized MD simulation workflows

  • Drug Discovery Pipeline: Virtual screening and ADMET prediction

  • Chemical Kinetics: Reaction rate analysis and mechanism studies

Support & Community

Keywords for Search Engines

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