这是gromacs报错信息
There are inconsistent shifts over periodic boundaries in a molecule type consisting of 3 atoms.
The longest distance involved in such interactions is 5.411 nm which is above half the box length.
Either you have excessively large distances between atoms in bonded interactions or your system is exploding.
There is no domain decomposition for 36 ranks that is compatible with the given box and a minimum cell size of 15.9594 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
这是packmol 的输入文件
structure bs-12.pdb
number 1
atoms 38
inside box 0. 0. 32. 67. 67. 35
end atoms
atoms 48
inside box 0. 0. 17. 67. 67. 18
end atoms
end structure
structure water.pdb
number 7000
inside box 0. 0. 35. 69. 69. 105
end structure
structure Na.pdb
number 120
inside box 0. 0. 35. 69. 69. 105
end structure
structure Cl.pdb
number 120
inside box 0. 0. 35. 69. 69. 105
end structure
structure bs-12.pdb
number 1
atoms 38
inside box 0. 0. 105. 67. 67. 108
end atoms
atoms 48
inside box 0. 0. 122. 67. 67. 123
end atoms
end structure