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本帖最后由 LiJiatong 于 2021-11-29 11:05 编辑
在进行mdrun的时候,总是报错,Fatal error :
1 of the 9386 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.211 nm) or the two-body cut-off distance (1.211 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
是我的mdp设置有问题吗?(下为md.mdp)
title = Martini MD
integrator = md
dt = 0.02
nsteps = 250000000
nstcomm = 100
comm-grps = DPPC W
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 1000
nstenergy = 1000
nstxout-compressed = 1000
compressed-x-precision = 100
compressed-x-grps = DPPC W
energygrps = DPPC W
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.1
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1
tcoupl = v-rescale
tc-grps = DPPC W
tau_t = 1.0 1.0
ref_t = 305 305
Pcoupl = parrinello-rahman
Pcoupltype = semiisotropic
tau_p = 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 305
gen_seed = 473529
Dispcorr = Enerpres
nstcalcenergy = -1
continuation = yes
constraints = none
constraint_algorithm = Lincs
;lincs_order = 4
;lincs_warnangle= 30
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