求助：在做能量最小化时出现错误

TOPGAO

如题：
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 8 atoms. The longest distance involved in such interactions is
8.640 nm which is above half the box length. Either you have excessively large
distances between atoms in bonded interactions or your system is exploding.

增大盒子后，相互涉及的的距离也会变大，该如何解决

sobereva

上传结构文件和mdp，否则没法判断

TOPGAO

老师，我想做的是两个肽的共组装，粗粒化后用packmol批量生成，文件如下，带水的结构文件太大传不上来
在加离子之前生成tpr时，报如下错误：
Warning: atom name 10 in topol.top and protein_sol.gro does not match (BB - SC1)
Warning: atom name 11 in topol.top and protein_sol.gro does not match (SC1 - BB)
Warning: atom name 12 in topol.top and protein_sol.gro does not match (SC2 - SC1)
Warning: atom name 13 in topol.top and protein_sol.gro does not match (BB - SC2)
Warning: atom name 14 in topol.top and protein_sol.gro does not match (SC1 - SC3)
Warning: atom name 15 in topol.top and protein_sol.gro does not match (SC2 - BB)
Warning: atom name 16 in topol.top and protein_sol.gro does not match (SC3 - SC1)
Warning: atom name 17 in topol.top and protein_sol.gro does not match (BB - SC2)
Warning: atom name 18 in topol.top and protein_sol.gro does not match (BB - SC3)
Warning: atom name 19 in topol.top and protein_sol.gro does not match (SC1 - BB)
Warning: atom name 20 in topol.top and protein_sol.gro does not match (SC2 - BB)
Warning: atom name 21 in topol.top and protein_sol.gro does not match (BB - SC1)
Warning: atom name 22 in topol.top and protein_sol.gro does not match (SC1 - SC2)
Warning: atom name 23 in topol.top and protein_sol.gro does not match (SC2 - BB)
Warning: atom name 24 in topol.top and protein_sol.gro does not match (SC3 - SC1)
Warning: atom name 25 in topol.top and protein_sol.gro does not match (BB - SC2)
Warning: atom name 26 in topol.top and protein_sol.gro does not match (BB - SC3)
Warning: atom name 27 in topol.top and protein_sol.gro does not match (SC1 - BB)
Warning: atom name 28 in topol.top and protein_sol.gro does not match (SC2 - SC1)
Warning: atom name 34 in topol.top and protein_sol.gro does not match (BB - SC1)
(more than 20 non-matching atom names)

WARNING 2 [file topol.top, line 17]:
  1660 non-matching atom names
  atom names from topol.top will be used
  atom names from protein_sol.gro will be ignored

然后运行的时候就报上面那个错误