求助：做能量最小化时报错

FrancisLi

我在跑液体系统，之前都是packmol直接生成一个很松散，分子间距很大的pdb文件去gmx里跑，今天突发奇想直接用packmol生成一个很致密的液体pdb，分子间距很小，但是在gmx做能量最小化的时候报错：

1. Step -1:
   
2. Atom 43788 moved more than the distance allowed by the domain decomposition (3.025000) in direction X
   
3. distance out of cell -8.729988
   
4. New coordinates:   -5.705    1.495    6.319
   
5. Old cell boundaries in direction X:    3.025    6.050
   
6. New cell boundaries in direction X:    3.025    6.050
   
7. 
   
8. -------------------------------------------------------
   
9. Program:     gmx mdrun, version 2021.3
   
10. Source file: src/gromacs/domdec/redistribute.cpp (line 217)
    
11. MPI rank:    4 (out of 4)
    
12. 
    
13. Fatal error:
    
14. One or more atoms moved too far between two domain decomposition steps.
    
15. This usually means that your system is not well equilibrated
    
16. 
    
17. For more information and tips for troubleshooting, please check the GROMACS
    
18. website at http://www.gromacs.org/Documentation/Errors
    
19. -------------------------------------------------------

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想问下各位老师，这种情况有什么办法吗，还是只能先从松散的pdb文件开始跑？感谢！

sobereva

是。另见http://sobereva.com/soft/Sobtop#FAQ8

FrancisLi

sobereva 发表于 2022-7-28 20:24
是。另见http://sobereva.com/soft/Sobtop#FAQ8

哦哦好的！感谢sob老师！