标题: gromacs平衡时遇到cut-off过长怎么办 [打印本页] 作者Author: 笨笨鸟 时间: 2025-8-30 20:37 标题: gromacs平衡时遇到cut-off过长怎么办 计算N2在ZIF-8中的扩散，能量最小化过程正常，但平衡时报错Fatal error:
The pair-list cut-off (87.719 nm) is longer than half the shortest box vector or longer than the smallest box diagonal element (1.6991 nm). Increase the box size or decrease nstlist or increase verlet-buffer-tolerance，检查了mdp文件设置的rlist为1.2nm，确实小于盒子长度（3.39820nm）的一半，但为什么计算出的pair-list cut-off (87.719 nm)这么大呢，试着减小rlist 或nstlist，仍然是这种报错，请问是哪里有问题呢？
mdp相关设置：
em.mdp
nstlist = 10 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
periodic-molecules = yes