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标题: 关于模拟晶体表面吸附时盒子体积骤增的问题 [打印本页]

作者
Author: huangfuxin 时间: 2020-11-18 13:32
标题: 关于模拟晶体表面吸附时盒子体积骤增的问题
小弟正在搞两层蒙脱石晶体吸附有机物，蒙脱石晶体除OH全被FREEZE，负电荷由金属阳离子填充，溶剂为水。初始结构由图1所示；
可是我在控温控压条件下，模拟过程中盒子体积不断增加，直接跑到外太空去了，原本3.888×3.29×7.29nm的盒子，在15ns时，xyz每个方向长度甚至都增加到了20倍
1.请教一下是我mdp有什么问题吗？
2.此外，体系中的晶体部分理论上是无限延展的嘛，那周期性边界中periodic-molecules有没有必要设置为yes呢
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md.mdp

; Run parameters
integrator = md                ; leap-frog integrator
nsteps = 7500000          ; 1 fs * 100000 = 100 ps 15ns
dt = 0.002 ; 1 fs
; Output control
nstxout = 2000 ; save coordinates every 1 ps
nstvout = 2000 ; save velocities every 1 ps
nstxtcout = 2000                ; xtc compressed trajectory output every 1 ps
nstenergy = 2000          ; save energies every 1 ps
nstlog = 2000 ; update log file every 1 ps
constraints = none
continuation = no
constraint_algorithm = lincs
lincs_iter = 1
lincs_order = 4
; Neighborsearching
cutoff-scheme          = Verlet ; search neighboring grid cels
ns-type                = Grid
nstlist = 10          ; 10 fs
rlist = 1.2                   ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2                   ; short-range electrostatic cutoff (in nm)
rvdw = 1.2                   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4
fourierspacing = 0.16
; Temperature coupling is on
tcoupl = V-rescale          ; modified Berendsen thermostat
tc-grps = System             ; two coupling groups - more accurate
tau_t = 0.1                   ; time constant, in ps
ref_t = 300             ; reference temperature, one for each group, in K

; Pressure coupling is on
; Pressure coupling is on
pcoupl                = Berendsen
pcoupltype             = Isotropic
tau_p                = 2.0
ref_p                = 1.0
compressibility       = 4.5e-5             ;                   ; isothermal compressibility of water, bar^-1
refcoord_scaling       = com

; Periodic boundary conditions
pbc = xyz          ; 3-D PBC

; Velocity generation
gen_vel = yes
gen_temp = 300

freezegrps = MMT_NOOH
freezedim = Y Y Y

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FIG.1：初始结构；
FIG.2 FIG.3 ：模拟中的片段
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作者
Author: sobereva 时间: 2020-11-18 18:51
你这体系都没必要控压，而且就算要控压也应当是半各项同性控压
freeze结合控压容易出问题，非要限定位置又要用压浴应当用位置限制势
gen_vel结合较高的初始温度是不良做法，容易崩
用periodic-molecules = yes
“负电荷由金属阳离子填充”语义不明

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