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本帖最后由 jlyjlysjd 于 2024-6-14 14:48 编辑
我的产生相阶段使用命令:
gmx grompp -f prd.mdp -o prd -pp prd -po prd -c eql -t eql后报了这个错。
我是加入了nstvout= 500后就报错了,不太明白这个错误Did not find a frame with coordinates in file eql.trr意味着什么,请各位老师帮助。
另外同时有一个警报:WARNING: Did not find a frame with velocities in file eql.trr, all velocities will be set to zero! 不太能理解为什么会没有速度呢?
我是想做速度自相关的,但是自从加入了记录速度以后就开始报错了,请老师们帮我看看问题出在哪里了呢?
附:eql.mdp:
integrator = md
dt = 0.002
nsteps = 5000000
nstenergy = 500
nstlog = 500
nstxout-compressed = 1000
nstvout = 500
nstfout = 500
constraint-algorithm = lincs
constraints = h-bonds
annealing = single
annealing_npoints = 7
annealing_time = 0 1000 2000 3000 4000 5000 7000
annealing_temp = 0 500 500 400 400 298.15 298.15
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
DispCorr = EnerPres
tcoupl = V-rescale
tc-grps = System
tau-t = 0.2
ref-t = 298.15
pcoupl = C-rescale
tau_p = 1.0
compressibility = 8.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 298.15
gen_seed = -1
这里做完能量最小化以后,我让每一个离子都产生了一个速度,eql运行完后,每一个粒子是不是应该都有了一个自己的速度呢?
prd.mdp:
integrator = md
dt = 0.002 ; 2 fs
nsteps = 5000000 ; 5.0 ns
nstenergy = 5000
nstlog = 5000
nstxout-compressed = 2000
nstvout = 5000
nstfout = 5000
continuation = yes
constraint-algorithm = lincs
constraints = h-bonds
pbc = xyz
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
DispCorr = EnerPres
tcoupl = V-rescale
tc-grps = System
tau-t = 0.2
ref-t = 298.15
pcoupl = C-rescale
tau_p = 1.0
compressibility = 8.5e-5
ref_p = 1.0
gen_vel = no
在产生相这里我就设定为了no,想让粒子继续按着原有的速度模拟,但是就出现了上文的错误,请问这是怎么回事呢?
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