Molecular Modeling in Docker

This repository contains a Dockerfile for building a molecular dynamics simulation and quantum chemistry base environment with CUDA support. The container includes various tools for molecular modeling, analysis, and visualization and X11 forwarding configured.

Included Software

• GROMACS 2023.5: Molecular dynamics package with CUDA support
• AutoDock Vina 1.2.5: Molecular docking program
• Multiwfn 3.8: Wavefunction analysis tool by Dr. Tian Lu (Contact: sobereva[at]sina.com. Beijing Kein Research Center for Natural Sciences 北京科音自然科学研究中心)
• Sobtop: Molecular topology tool by Dr. Tian Lu (Contact: sobereva[at]sina.com. Beijing Kein Research Center for Natural Sciences 北京科音自然科学研究中心)
• Avogadro 2: Advanced molecular editor
• xTB 6.7.1: Semi-empirical quantum chemistry package
• MGLTools 1.5.7: Molecular graphics tools
• PyMOL: Molecular visualization system
• OpenBabel: Chemical toolbox
• Additional Tools: pdb2pqr, gmx_MMPBSA, DuIvyTools

System Requirements

• Docker desktop and VcXsrv installed on your system You can find the download here：https://vcxsrv.com/
• NVIDIA GPU with CUDA support

Running the Container

docker build -t cadd:v0 -f .\CADD.dockerfile .
docker run -it --gpus all -e DISPLAY=host.docker.internal:0 -v ${PWD}:/home/cadd/test cadd:v0 /bin/bash # Mount the current location to this address inside the container /home/cadd/test

Container Features

GPU Acceleration

• CUDA-enabled GROMACS installation
• Optimized FFTW library with AVX2 support
• GPU-specific environment variables pre-configured

GUI Application Support

• Avogadro 2 for molecular editing
• PyMOL for visualization
• X11 forwarding configured

Development Environment

• Build tools and compilers included
• Python environment with scientific packages
• Common molecular modeling libraries

Directory Structure

The main software packages are installed in /home/cadd/Software/ with the following structure:

/home/cadd/Software/
├── ADT/                 # MGLTools
├── GMX-2023.5/         # GROMACS
├── Multiwfn/           # Multiwfn
├── Sobtop/            # Sobtop
├── Vina/              # AutoDock Vina
├── xTB/               # xTB package
└── FFTW/              # FFTW library

Environment Variables

The container comes with pre-configured environment variables for optimal performance:

• GMX_GPU_DD_COMMS=true
• GMX_GPU_PME_PP_COMMS=true
• GMX_FORCE_UPDATE_DEFAULT_GPU=true
• All necessary PATH variables for installed software

Troubleshooting

1. GPU Access Issues
   • Verify NVIDIA drivers are properly installed
   • Check NVIDIA Container Toolkit installation
   • Ensure docker daemon configuration includes NVIDIA runtime

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.