各位老师好，请教distance_restraints报错的问题，谢谢老师

cgy · 发表于 Post on 2024-12-9 11:51:21

本帖最后由 cgy 于 2024-12-10 11:43 编辑

  各位老师好，在学习了论坛中关于距离限制的帖子后，我也对同一分子下的三层二硫化钼纳米片的边缘原子进行距离限制以使纳米片不跑散，但总报错如下
ERROR 1 [file m443.itp, line 8]:
  Atom index (5) in distance_restraints out of bounds (1-0).
  This probably means that you have inserted topology section
  "distance_restraints"
  in a part belonging to a different molecule than you intended to.
  In that case move the "distance_restraints" section to the right molecule.
我在top文件中二硫化钼纳米片的itp文件行的前后加了if define，如下
#include "D:\M443\pip.itp"
#ifdef DISRES
#include "D:\M443\m443.itp"
#endif
#include "oplsaa.ff/tip3p.itp"

在itp文件中将[ distance_restraints ]放到了[ moleculetype ]之后
[ moleculetype ]
; name       nrexcl
m443    3
[ distance_restraints ]
5 2 1 0 1 0.33 0.35 0.35 1.0
11 8 1 1 1 0.33 0.35 0.35 1.0
...

在mdp文件中加了
define = -DDISRES
dihre = simple
disre-weighting       = Conservative
disre-mixed             = no
disre-fc                   = 1000
disre-tau                = 0
nstdisreout             = 100

请问老师该如何解决，谢谢老师。