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本帖最后由 夜夜衣 于 2020-6-22 09:58 编辑
各位老师，我再做一个富集的课题，使用gromacs nvt系综模拟 CNT （18，0 半径为1.25nm，长度为5.112nm） 和1000个H2或者N2在等温300K不同压强下的吸附（碳管固定），但是总是会出现异常吸附的情况， 主要是在低压的情况下 p=0.1Mpa-1Mpa，（正方体盒子的边长在34nm-16nm）之间， 异常情况就是 在低压下，碳管内部不应该吸附那么多分子，而模拟中却能吸附很多分子。经过测试，发现是 nstcomm 这个参数的问题，在氢气的体系，nstcomm = 默认的100， 正常（0.1MPa吸附较少分子，且吸附量随着压强增加而增加 如果nstcomm=5 管内能吸附特别多的分子，表明扩散很快； 但是N2的体系相反，nstcomm = 默认的100 吸附量异常多，并且50ns还没有平衡，nstcomm=5时就吸附不上分子了，实在是闹不明白是什么原因引起的这个现象，因为后期我要做两个气体混合的吸附模拟，所以想弄明白是什么原因导致的，轨迹也看不出比较明显的问题，下面是mdp文件，我能否通过尝试不同的nstcomm去找到一个适用于两个体系的值呢？我查询手册 nstcomm 是frequency for center of mass motion removal，这个会影响吸附吗，求各位老师解惑，万分感谢
; VARIOUS PREPROCESSING OPTIONS，
define =
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0
dt = 0.001
nsteps = 50000000
init_step = 0
comm_mode = Linear
nstcomm = 100 （）
comm-grps = system
; OUTPUT CONTROL OPTIONS
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = -1
nstenergy = 2000
nstxtcout = 2000
xtc-precision = 2000
xtc-grps =
energygrps = CNT NTR
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = Group
nstlist = 5
ns_type = grid
pbc = xyz
periodic_molecules = no
;verlet-buffer-drift = -1
rlist = 1.2
rlistlong = -1
nstcalclr = -1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = cut-off
coulomb-modifier = None
rcoulomb = 1.2
; Method for doing Van der Waals
vdw-type = cut-off
vdw-modifier = None
rvdw = 1.2
DispCorr = no
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.16
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = V-rescale
nsttcouple = -1
tc-grps = system
tau-t = 0.1
ref-t = 300
; Pressure coupling
Pcoupl = no
Pcoupltype = Isotropic
tau-p = 2.0
compressibility = 4.5e-5
ref-p = 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = com
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = yes
gen-temp = 300
gen-seed = 173529
; OPTIONS FOR BONDS
constraints = all-bonds
constraint-algorithm = Lincs
continuation = no
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 2
lincs-warnangle = 30
; ENERGY GROUP EXCLUSIONS
energygrp_excl = CNT CNT
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps = CNT
freezedim = Y Y Y
cos-acceleration =
deform =
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发表于 Post on 2020-6-18 14:38:55
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