動力學模擬時拓撲文件不能被讀取 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意味著mdrun用的輸入輸出文件的名字都是test，即當前目錄下得有test.tpr。這跟拓撲文件沒關(guān)系
用make_ndx給分子中結(jié)構(gòu)分組問題 改成group、加上-n index.ndx，就可以成功算D/A間的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程序計算出現(xiàn)的錯誤提示 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 你沒用-s指定.tpr文件名，于是程序自動嘗試用topol.tpr作為文件名，但是當前目錄下又不存在topol.tpr所以報錯。注意理解屏幕提示
Tutorial: Molecular dynamics (MD) simulation using Gromacs
蛋白質(zhì)復(fù)合物體系兩條鏈中pdb2gmx的拓撲文件參數(shù)設(shè)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進階】蛋白質(zhì)-共價抑制劑體系(含非標準殘基)MD模擬教程
GMX grompp
GROMACS教程2：蛋白-配體復(fù)合物（Protein-Ligand Complex）
GROMACS運行參數(shù)整理（二）
“Fatal error: Group SOLV referenced in the .mdp file was not found in the index file.” Help with SLURM HPC
Gromacs相關(guān)基礎(chǔ)知識
做蛋白-配體結(jié)合報錯Group Protein_UNL在index文件中沒有找到
用gromacs做傘狀采樣
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
