gmx_MMPBSA使用经验

　　记录一下gmx_MMPBSA的可视化经验。

工作环境

安装Miniconda

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

chmod +x Miniconda3-latest-Linux-x86_64.sh

./Miniconda3-latest-Linux-x86_64.sh

安装依赖

# 更新conda
conda update conda

# 创建激活gmxMMPBSA环境
conda create -n gmxMMPBSA python=3.11.8 -y -q
conda activate gmxMMPBSA

#安装mpi4py和AmberTools
conda install -c conda-forge "mpi4py=4.0.1" "ambertools<=23.3" -y -q

#安装绘图库
conda install -c conda-forge "numpy=1.26.4" "matplotlib=3.7.3" "scipy=1.14.1" "pandas=1.5.3" "seaborn=0.11.2" -y -q

#安装PyQt6
python -m pip install "pyqt6==6.7.1"

#安装GROMACS
conda install -c conda-forge "gromacs<=2023.4" pocl -y -q

安装gmx_MMPBSA

python -m pip install gmx_MMPBSA

使用

准备

参考链接

Installing gmx_MMPBSA

gmx_MMPBSA计算Gromacs分子动力学模拟中的结合自由能