BioExcel Use Case 1: collection of output data from molecular dynamics simulation

The Use Case aims to address all the challenges related to antibody design through an integrative approach combining the core BioExcel software comprising of GROMACS, HADDOCK and PMX.

The folder  contains the GROMACS output files (xtc and pdb file). Molecular Dynamics simulations have been performed with GROMACS version 2020 and CHARMM36 force field. The input files and scripts of the final protocol are publicly available on BioExcel GitHub https://github.com/bioexcel/BioExcel-UseCase1.

The Use Case 1 protocol was presented at the BioExcel Summer School on Biomolecular Simulation in 2021 (see https://doi.org/10.5281/zenodo.7009238 or https://youtu.be/_TDKfKX4kwM)

本用例旨在通过整合BioExcel核心软件（包含GROMACS、HADDOCK与PMX）的一体化方案，解决与抗体设计相关的所有挑战。

本文件夹包含GROMACS的输出文件（xtc与pdb格式文件）。本次研究采用GROMACS 2020版本与CHARMM36力场完成了分子动力学模拟。最终方案的输入文件与脚本已在BioExcel GitHub仓库https://github.com/bioexcel/BioExcel-UseCase1 公开获取。

本用例1的方案已于2021年BioExcel生物分子模拟暑期学校中展示（详见https://doi.org/10.5281/zenodo.7009238 或 https://youtu.be/_TDKfKX4kwM）。