Improving Aptamer Binding Affinity for HN Protein of Newcastle Disease Virus: Molecular Dynamics Simulations and MM/GBSA Calculations studies

Data Description: (1) All data uploaded to this database only represent the input and output files of the current research, including files from two parts: molecular dynamics simulations and binding free energy calculations. (2) Due to the large size of the original dynamics trajectories and intermediate files generated during binding free energy calculations, which exceed 50GB and cannot be uploaded, we have cleaned the data. The dynamics trajectories have undergone periodic correction and elimination of translation and rotation (fit.xtc). (3) Additionally, we have provided parameter files, log files, tpr files, top files, etc., throughout the molecular dynamics simulation process. Researchers can reproduce the simulations at any time using the current parameter files. (4) The parameter files for the binding free energy calculation part have also been provided (mmpbsa.in). Other parameter files used can be found in the molecular dynamics simulation folder.数据集说明：(1) 上传至本数据库的所有数据仅为本研究的输入与输出文件，涵盖分子动力学模拟（molecular dynamics simulations）与结合自由能计算（binding free energy calculations）两部分相关文件。(2) 由于原始动力学轨迹文件及结合自由能计算过程中生成的中间文件总容量超过50GB，无法直接上传，故对数据进行了清洗处理：已针对动力学轨迹文件完成周期性校正，并移除了平动与转动效应（fit.xtc）。(3) 此外，本数据集还提供了分子动力学模拟全流程的参数文件、日志文件、tpr文件、top文件等辅助材料，研究人员可通过当前提供的参数文件随时复现模拟过程。(4) 结合自由能计算模块的参数文件（mmpbsa.in）亦已同步提供，其余所需参数文件可在分子动力学模拟文件夹中获取。