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标题: 液液两相体系建模问题 [打印本页]

作者
Author: 孙宝刚 时间: 2020-7-18 21:49
标题: 液液两相体系建模问题
老师好，我向建立一个有机相与水相的两相体系（两相体积相同），想用packmol建模，怎么选择插入的有机分子数量和水分子的数量呢。我之前试过500水分子500有机物分子在做NPT（只控制z方向压强）时盒子在z方向变得很长而且水分子也散开（有机物分子没有散）如图。请老师指点

npt.mdp内容如下：
cpp                =  cpp
constraints       = all-bonds
constraint_algorithm =  LINCS
integrator       =  md
dt                =  0.0002
nsteps             =  500000
nstxout          =  200
nstvout          =  200
nstfout          =  200
nstlog             =  200
nstenergy          =  200
nstxtcout          =  2000
nstlist          =  10
ns_type          =  grid
coulombtype       =  PME
rlist             =  0.9
rcoulomb          =  1.0
rvdw             =  1.0
pbc                = xyz
optimize_fft       = yes
nstcomm          = 1
comm-grps          = system
; Berendsen temperature coupling is on
tcoupl             =  v-rescale
tc-grps          =  system
tau_t             =  0.1
ref_t             =  298
; Semiisotropic pressure coupling is now on
Pcoupl             =  Parrinello-Rahman
Pcoupltype       =  semiisotropic
tau_p             =  2.0
compressibility    =  0 4.5e-5
ref_p             =  1.0 1.0
energygrps       =  system
; Generate velocites is on at 300K.
gen_vel          =  yes
gen_temp          =  298
gen_seed          =  173529
periodic_molecules  = yes

作者
Author: sobereva 时间: 2020-7-18 22:41
根据纯物质状态的质量密度、分子质量，换算成加入的有机分子和水分子数

绝对不要用constraints       = all-bonds，公社论坛之前我回复过很多次

dt                =  0.0002莫名其妙，用这么小步长干嘛，一般都用0.002

若无特殊情况，rlist也设成1.0

体系都还没平衡，甭用PR压浴

甭用gen_vel          =  yes。老老实实从0K线性升温

periodic_molecules  = yes根本就不是用在当前场合的

你的mdp问题太多，不懂的不要瞎写

作者
Author: 孙宝刚 时间: 2020-7-19 14:06
Sob老师我计算了分子的实际数量。盒子大小为50 50 100，有机相与水相等体积得出水分子为836个甲苯分子为142个。并且修改了npt的mdp文件，NPT后得到下图，水分子与甲苯分子在横向汇集不知道哪里错了请老师指点。
npt.mdp内容如下

define                = -DPOSRES  ; position restrain the p507
constraints       = h-bonds
constraint_algorithm =  LINCS
integrator       =  md
dt                =  0.002
nsteps             =  500000
nstxout          =  200
nstvout          =  200
nstfout          =  200
nstlog             =  200
nstenergy          =  200
nstxtcout          =  2000
nstlist          =  10
ns_type          =  grid
coulombtype       =  PME
rlist             =  1.0
rcoulomb          =  1.0
rvdw             =  1.0
pbc                = xyz
optimize_fft       = yes
nstcomm          = 1
comm-grps          = system
; Berendsen temperature coupling is on
tcoupl             =  v-rescale
tc-grps          =  system
tau_t             =  0.1
ref_t             =  300
; Semiisotropic pressure coupling is now on
Pcoupl             =  Berendsen
Pcoupltype       =  semiisotropic
tau_p             =  2.0
compressibility    =  0 4.5e-5
ref_p             =  1.0  1.0       ;
energygrps       =  system
; Generate velocites is on at 300K.
gen_vel          =  no

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