动力学模拟时拓扑文件不能被读取 Invalid input values In option s Required option was not provided, and the default file ‘topol’ does not exist or is not accessible. The following extensions were tried to complete the file name: .tpr gmx mdrun -v -deffnm test意味着mdrun用的输入输出文件的名字都是test，即当前目录下得有test.tpr。这跟拓扑文件没关系
蛋白质复合物体系两条链中pdb2gmx的拓扑文件参数设置 gro格式就不体现链的信息
用make_ndx给分子中结构分组问题 改成group、加上-n index.ndx，就可以成功算D/A间的RDF了（gmx rdf -f final.xtc -s final.tpr -n index.ndx -ref ‘res_com of group D’ -sel ‘res_com of group A’）
用gromacs程序计算出现的错误提示 In option s Required option was not provided, and the default file ‘topol’ does not exist or is not accessible. The following extensions were tried to complete the file name: .tpr 你没用-s指定.tpr文件名，于是程序自动尝试用topol.tpr作为文件名，但是当前目录下又不存在topol.tpr所以报错。注意理解屏幕提示
Tutorial: Molecular dynamics (MD) simulation using Gromacs
蛋白质复合物体系两条链中pdb2gmx的拓扑文件参数设置
gmx mdrun error: “Error in user input: Invalid input values In option s”
Group Non-Protein referenced in the .mdp file was not found in the index file.
【GROMACS进阶】蛋白质-共价抑制剂体系(含非标准残基)MD模拟教程
GMX grompp
GROMACS教程2：蛋白-配体复合物（Protein-Ligand Complex）
GROMACS运行参数整理（二）
“Fatal error: Group SOLV referenced in the .mdp file was not found in the index file.” Help with SLURM HPC
Gromacs相关基础知识
做蛋白-配体结合报错Group Protein_UNL在index文件中没有找到
用gromacs做伞状采样
Fatal error: Group Non-Protein referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the ‘-n’ option of grompp
