GROMACS模拟离子液体水溶液遇到的问题

[Qing He版主]

大家好，有个问题想请教各位。我想观察离子液体[Omim]Cl在水溶液中的聚集现象，但最终结果没看出来胶束结构，想让大家帮忙看看我的方法和参数哪里有问题需要改进，谢谢啦！模拟最终结构如下（红点为水分子）：

 

建模是用PACKMOL在边长4.2nm方盒内放20个[Omim]Cl和2220个水分子（浓度0.5M），用ATB生成的拓扑文件GROMOS力场下模拟，先进行em，然后直接成品md（1ns），后来觉得可能时间不够长，又跑了1ns，结果还是差不多这样子…md.mdp如下：

define =
integrator = md
dt = 0.002
nsteps = 500000
comm_mode = linear
nstcomm = 100
comm-grps = system
energygrps =
;
; output frequency
nstxout = 500
nstvout = 500
nstfout = 0
nstlog = 500
nstenergy = 500
nstxtcout = 500
xtc_grps = system
;
annealing = single
annealing_npoints = 2
annealing_time = 0 50
annealing_temp = 0 298.15
;
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2
cutoff-scheme = group
coulombtype = PME
rcoulomb = 1.2
vdwtype = cut-off
rvdw = 1.2
DispCorr = EnerPres
;
Tcoupl = v-rescale
tau_t = 0.2
tc_grps = system
ref_t = 298.15
;
Pcoupl = Berendsen
pcoupltype = isotropic ;semiisotropic
tau_p = 0.5
ref_p = 1.0
compressibility = 4.5e-5
;
gen_vel = no
gen_temp = 298.15
gen_seed = -1
;
freezegrps =
freezedim =
constraints = hbonds
constraint_algorithm = LINCS
implicit_solvent = no
E_x =
E_y =
E_z =


还有个问题就是由于周期性边界条件存在，经常有分子从边界一边瞬移到另一边，最后用VMD做模拟过程视频的时候边缘部分一闪一闪的看着很奇怪，有什么方法可以解决这个问题吗？谢谢！

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[Qing He版主]

[caption id="attachment_238" align="alignnone" width="540"] GROMACS模拟离子液体水溶液[/caption]

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