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 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！ (, 下载次数 Times of downloads: 0)