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GROMACS 入门

2019-01-22 18:11:28

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GROMACS 入门

GROMACS 安装

  • 安装：

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    wget https://ftp.gromacs.org/gromacs/gromacs-2023.tar.gz
    tar -zxvf gromacs-2023.tar.gz
    cd gromacs-2023
    mkdir build
    cd build
    export CMAKE_PREFIX_PATH=~/fftw # fftw 路径
    cmake .. -DCMAKE_INSTALL_PREFIX=~/softwares/gromacs # gromacs安装路径
    make install -j8

  • 最新快速安装：

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    tar xfz gromacs-2023.2.tar.gz
    cd gromacs-2023.2
    mkdir build
    cd build
    # 这里自动build一个fftw
    cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=~/softwares/gromacs
    make
    make check
    sudo make install

  • 如果使用的是 Ubuntu 操作系统，只需在终端执行以下命令即可：

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    sudo apt-get install gromacs

  • 环境变量设置：

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    cd ~/softwares/gromacs/bin
    pwd # 查看路径，并复制
    sudo vim ~/.bashrc
    export PATH="~/softwares/gromacs/bin:$PATH"
    # esc
    # :
    # wq
    source ~/.bashrc

  • 测试：

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    gmx -version
    # output:
    # Executable:   ~/softwares/gromacs/bin/gmx
    # Data prefix:  ~/softwares/gromacs
    # Working dir:  ~/softwares/gromacs
    # Command line:
    #   gmx -version
    # 
    # GROMACS version:    2023-dev
    # Precision:          mixed
    # Memory model:       64 bit
    # MPI library:        thread_mpi
    # OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)
    # GPU support:        disabled
    # SIMD instructions:  AVX2_256
    # CPU FFT library:    fftw-3.3.10
    # GPU FFT library:    none
    # Multi-GPU FFT:      none
    # RDTSCP usage:       enabled
    # TNG support:        enabled
    # Hwloc support:      disabled
    # Tracing support:    disabled
    # C compiler:         /usr/bin/cc GNU 9.4.0
    # C compiler flags:   -Wno-array-bounds -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wextra -Wno-sign-compare -Wpointer-arith -Wundef -Werror=stringop-truncation -Wno-missing-field-initializers -O3 -DNDEBUG
    # C++ compiler:       /usr/bin/c++ GNU 9.4.0
    # C++ compiler flags: -Wno-array-bounds -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wall -Wextra -Wpointer-arith -Wmissing-declarations -Wundef -Wstringop-truncation -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG
    # BLAS library:       External - detected on the system
    # LAPACK library:     External - detected on the system

  • 参考：

运行GROMACS

运行GROMACS 所需文件

  • 初始构型文件：x.gro x.pdb
  • 参数控制文件：x.mdp
  • 力场文件：x.top x.itp
  • 索引文件：x.ndx

相关力场：

  • Martini粗粒化力场

  • AMBER、CHARMM、OPLS-AA、GROMOS

力场文件相关工具：

  • pdb2gmx、AMBER Tool、tppmktop、x2top、martini.py、ATB/PRODRG……

后处理工具：

  • gmx msd
  • gmx rdf
  • gmx totcf (旋转自相关函数)
  • gmx potential (静电势)
  • gmx helix ($\alpha$螺旋结构的基本性质)
  • MD_Analysis、VMD
  • 自编程
Tags: GROMACS GROMACS入门
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