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标题: NVT系综平衡时跑一段时间就报错，然后就停了 [打印本页]

作者
Author: 木林森 时间: 2021-1-25 20:19
标题: NVT系综平衡时跑一段时间就报错，然后就停了
最近在跑nvt系综时，跑大约100ps就停了，报错：
1 of the 57972 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
有人可以帮忙解决下吗？

这是我用的mdp文件：
title          = NVT simulation
cpp          = /usr/bin/cpp
integrator    = md
dt             = 0.0020 ; ps !
nsteps       = 7500000;

nstxout       = 1000 ; collect data every 2.0 ps
nstvout       = 0
nstfout       = 0
nstlist       = 5
ns_type       = grid
rlist          = 1.2

cutoff-scheme = Verlet
coulombtype    = PME
rcoulomb       = 1.2
rvdw          = 1.2
pbc          = xyz
DispCorr       = EnerPres
fourierspacing  = 0.50
fourier_nx    = 0
fourier_ny    = 0
fourier_nz    = 0
pme_order    = 4
ewald_rtol    = 1e-5
optimize_fft = yes

; Berendsen temperature coupling is on in four groups
Tcoupl       = V-rescale
tc_grps       = System
tau_t          = 0.1
ref_t          = 300.0

; Pressure coupling is on
Pcoupl       = no ;parrinello-rahman
pcoupltype    = isotropic
tau_p          = 0.5
compressibility = 4.5e-5
ref_p          = 1.000

; Generate velocites is on at 300 K.
gen_vel       = no
gen_temp       = 298.0
gen_seed       = 94823

; Constrains of Bonds
constraints    = all-bonds
constraint_algorithm = lincs

; Groups
energygrps    = Flexible Frozen CS CL SOL
; Freeze
freezegrps    = Frozen
freezedim    = Y Y Y

作者
Author: sobereva 时间: 2021-1-25 20:50
绝对不要用all-bonds，论坛里我强调过多次

没特殊情况别自己改fourierspacing

仔细看轨迹，判断是否有异常
如果崩了，仔细检查拓扑文件、初始结构的合理性

作者
Author: 木林森 时间: 2021-1-25 21:22

sobereva 发表于 2021-1-25 20:50
绝对不要用all-bonds，论坛里我强调过多次

没特殊情况别自己改fourierspacing

谢谢sob老师，我再试试

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