求助gmx在100ps限制性动力学grompp时原子距离过大报错

wbqdssl

各位老师好，我在尝试用gromacs2024.5做蛋白-配体的分子动力学模拟。
蛋白配体的结构文件使用的是Desmond模拟300ns后最后一帧的结构，对于蛋白文件，用gmx pdb2gmx -f protein.pdb -o protein.gro  -ignh命令处理（因为是测试，力场瞎选的）；对于配体，用sobtop处理，将配体的文件合并到top文件后，依次使用如下命令：
gmx editconf -f complex.gro -o complex_box.gro -bt cubic -box 10 10 10

gmx solvate -cp complex_box.gro -o complex_sol.gro -p topol.top

gmx grompp -f em.mdp -c complex_sol.gro -p topol.top -o em.tpr -maxwarn 2
这个命令打完之后报WARNING 2 [file em.mdp]:
  The largest distance between excluded atoms is 1.504 nm between atom 8576
  and 8585, which is larger than the cut-off distance. This will lead to
  missing long-range corrections in the forces and energies. If you expect
  that minimization will bring such distances within the cut-off, you can
  ignore this warning.

gmx genion -s em.tpr -p topol.top -o system.gro -neutral

gmx grompp -f em.mdp -c system.gro -p topol.top -o em.tpr  -maxwarn 1

gmx mdrun -v -deffnm em -pin on -notunepme -ntmpi 1 -ntomp 12

这里输出
Polak-Ribiere Conjugate Gradients converged to machine precision in 193 steps,
but did not reach the requested Fmax < 100.
Potential Energy  =  3.1468682e+08
Maximum force     =  1.3912910e+09 on atom 20458
Norm of force     =  6.3254481e+06

gmx grompp -f pr.mdp -c em.gro -p topol.top -r em.gro -o pr.tpr
这里输出
ERROR 1 [file pr.mdp]:
  The largest distance between excluded atoms is 6.952 nm between atom 7246
  and 7261, which is larger than the cut-off distance. This will lead to
  missing long-range corrections in the forces and energies.


Fatal error:
There was 1 error in input file(s)


请问各位老师这是因为什么呢，换gromacs2023.2版本也报错，bash的日志和运行文件都上传了；恳请各位老师指点！
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sobereva

按照http://sobereva.com/soft/Sobtop#FAQ8说的一点点检查

wbqdssl

sobereva 发表于 2025-7-9 05:34
按照http://sobereva.com/soft/Sobtop#FAQ8说的一点点检查

好的，谢谢社长！