如下是我自用的一些Docker

1. gromacs-GPU Docker

自写gromacs Docker，CUDA版本12.1，gromacs版本 gromacs-2024.5

可从此下载：Dockerfile

# Use an official Ubuntu base image
FROM nvidia/cuda:12.1.1-devel-ubuntu22.04

# Set environment variables to avoid interactive prompts during installation
ENV DEBIAN_FRONTEND=noninteractive
SHELL ["/bin/bash", "-c"]

# Install dependencies
RUN apt-get update && && apt-get upgrade -y && apt-get install -y \
    libgomp1 \
    liblapack3 \
    openmpi-common \
    build-essential \
    cmake \
    python3 \
    wget \
    openmpi-bin \
    libopenmpi-dev \
    && apt-get clean && rm -rf /var/lib/apt/lists/*

# Set working directory
WORKDIR /usr/local/src

RUN echo "export OMPI_ALLOW_RUN_AS_ROOT=1" >> ~/.bashrc && \
    echo "export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1" >> ~/.bashrc  && \
    source ~/.bashrc

# Download and install GROMACS
RUN wget https://ftp.gromacs.org/gromacs/gromacs-2024.5.tar.gz && \
    tar xfz gromacs-2024.5.tar.gz && \
    cd gromacs-2024.5 && \
    mkdir build && cd build && \
    cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DGMX_MPI=on && \
    make -j$(nproc) && make install && \
    cd ../.. && rm -rf gromacs-2024.5*


# Source GROMACS
RUN echo "source /usr/local/gromacs/bin/GMXRC" >> ~/.bashrc

# Set entrypoint
# ENTRYPOINT ["gmx"]

运行例子：

docker run -it --rm --gpus all  -v $HOME/shiyan/zhangxuan/protein-ligand-md:$HOME/shiyan gromacs:2022

1. Dl_binder_design

自写的dl_binder_design 不包含rfdiffusion部分

可从此下载dl_binder_design.zip

# Use an official Python runtime as a parent image
FROM nvcr.io/nvidia/cuda:12.1.0-cudnn8-runtime-ubuntu22.04

# Set the working directory in the container
WORKDIR /app

COPY . /app


ENV PATH="/app/miniconda/bin:$PATH"

# Install Conda Mini (Miniconda)
RUN apt-get -q update && apt-get install -y wget git && \
    wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-py311_25.3.1-1-Linux-x86_64.sh -O miniconda.sh && \
    bash miniconda.sh -b -p /app/miniconda && /app/miniconda/bin/conda init bash  && \
    rm miniconda.sh && \
    /app/miniconda/bin/conda clean -a -y && cd dl_binder_design/ && \
    conda config --add channels https://levinthal:paradox@conda.graylab.jhu.edu && \
    conda config --add channels conda-forge && \
    cd include && conda env create -f proteinmpnn_fastrelax.yml && \
    conda env create -f af2_binder_design.yml && \
    cd ../mpnn_fr && git clone https://github.com/dauparas/ProteinMPNN.git && \
    cd ../af2_initial_guess/ && mkdir -p model_weights/params

WORKDIR /app/dl_binder_design

# Default command
CMD ["bash"]