04_HTMD_Cavity: Incorporating prior knowledge in the seeds of adaptive sampling molecular dynamics simulations of ligand transport in enzymes with buried active sites

# Contains input, output and restart files used for HTMD (High-throughput molecular dynamics) adaptive sampling simulations at 310K for Cavity schemes. # The forders are organized as: Input_files/ # Contains .parm7 and .rst files of 30 seed conformations obtained from equilibrations and used for adaptive sampling inputs, **run_adaptiveMD.py** : Script file executing the adaptive sampling using distance matrix considering protein C-alpha atoms and heavy atoms of DBE.rep1/└── adaptive_data/ ├── generators/ # Contains the initial generator files provided by the user │ ├── ../structure.parm7 │ ├── ../input.ncrst │ └── ... ├── input/ # Contains the files needed to start all simulations of all epochs (automatically generated) │ ├── ../equil1.log │ ├── ../input.ncrst │ └── ...└──rep2/......本数据集包含用于310K温度下空腔方案（Cavity schemes）的高通量分子动力学（High-throughput molecular dynamics, HTMD）自适应采样模拟所需的输入文件、输出文件及重启文件。 数据集文件夹组织形式如下： Input_files/：包含30个经平衡模拟获得的种子构象对应的.parm7与.rst格式文件，用于自适应采样输入；**run_adaptiveMD.py**：用于执行自适应采样的脚本文件，该脚本基于距离矩阵，以蛋白质Cα原子与DBE的重原子为计算考量对象。 rep1/ └── adaptive_data/ ├── generators/：存放用户提供的初始生成器文件，包含../structure.parm7、../input.ncrst等文件 ├── input/：存放启动所有模拟轮次所有模拟所需的自动生成文件，包含../equil1.log、../input.ncrst等文件 └── rep2/……