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标题: 在进行pull的时候是否需要对质心进行平转动限制？ [打印本页]

作者
Author: 姜酱将 时间: 2024-5-6 15:05
标题: 在进行pull的时候是否需要对质心进行平转动限制？
如题，我在进行pull时，想把右侧的油分子压入孔隙中，但出现了油侧油一进去，左侧的板子就会往左移动，我个人认为是为了保证质心的不变，所以左边的体系会往左走。如何避免这种情况，我想实现的是左右板子同时向中间压缩。下面是我的pull过程代码，请各位指点一下

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(, 下载次数 Times of downloads: 14)
; title    = constant-force
define    =
; Run parameters
integrator  = md
dt       = 0.00001
tinit    = 0
nsteps    = 1000000 ; 10 ps
nstcomm    = 1000
; Output parameters
nstxout    = 1000 ;
nstvout    = 1000
nstfout    = 1000
nstxout-compressed = 1000    ;
nstenergy = 1000
comm-grps =  middle  sgl       ;这里的sgl是我中间的孔隙
comm-mode =  Angular
; Bond parameters
;constraint_algorithm = lincs
;constraints          = h-bonds
;continuation          = yes    ; continuing from NPT
; Single-range cutoff scheme
cutoff-scheme = Verlet
;ns_type       = grid
rcoulomb       = 1.5
rvdw          = 1.5
; PME electrostatics parameters
coulombtype    = PME
; optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = V-rescale
tau_t = 0.2 0.2
tc_grps = vel fixed
ref_t = 418 418
;
; Pressure coupling is on
;Pcoupl       = Berendsen
;pcoupltype    = semiisotropic
;tau_p          = 5.0
;compressibility = 4.5e-5
;ref_p          = 1.0
;refcoord_scaling = com
; Generate velocities is off
gen_vel    = no
; Periodic boundary conditions are on in all directions
pbc    = xyz
; Long-range dispersion correction
DispCorr = no
;Pull code
pull                   = yes
pull-ngroups          = 3
pull-ncoords          = 2
pull-group1-name       = left
pull-group2-name       = right
pull-group3-name       = middle

pull-coord1-type       = constant-force
pull-coord1-geometry    = direction-periodic
pull-coord1-groups    = 1 3
pull-coord1-vec       = 1 0 0
pull-coord1-dim       = Y N N
pull-coord1-k          = 927.41 ; avoid forces working directly on this distance

pull-coord2-type       = constant-force
pull-coord2-geometry    = direction-periodic
pull-coord2-groups    = 2 3
pull-coord2-vec       = -1 0 0
pull-coord2-dim       = Y N N
pull-coord2-k          = 684    ; avoid forces working directly on this distance

;
freezegrps  = fixed left right
freezedim = y y y n y y n y y
constraints = hbonds

作者
Author: 姜酱将 时间: 2024-5-9 02:38
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