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各位老师 最近自学md，被md折磨的不行，请教几个关于top文件的问题，希望赐教
课题：H2 在碳纳米管内的富集效应。模型选用长5.112nm的CNT，直径1.4nm，气体分子使用用1000个H2分子。根据pv=nRT， 在定温300K下定压下V有定制，所以固定温度300K不变， 改变盒子大小来模拟不同的压强0.1Mpa下时边长34nm的正方体盒子，0.5Mpa下是边长20nm的盒子，以此类推。使用gromacs软件4.6.5，
问题1：在模拟中CNT冻住，那么CNT的itp文件是否只需要[ atoms ]这一部分，键和二面角不需要定义？
问题2. 由于我不想使用标准力场中的非键参数eps和sigma，该如何自定义我需要的原子类型和参数？ 可否在计算目录下自定义一个gas.ff文件，然后将我需要的原子参数，按照opls非键参数的格式定义我需要的原子然后再include呢？top下的非键和成键参数不能修改？
问题3：关于itp文件的格式，如下H2的itp， resnr和cgnr分别为残基序号和电荷组序号的书写有什么讲究？resnr全改为2 和 cgnr全改为1 这样操作有什么影响？例如下面CNT的itp（截取的一部分）， 另外 atom着一列我这样写可不可以 还是需要全部写成H而不是H1，H2
[ moleculetype ]
; Name nrexcl
HTR 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 opls_140 1 HTR H1 1 0 1.008
2 opls_140 1 HTR H2 2 0 1.008
[ bonds ]
1 2 1 0.74E-01 3.924592e+05
[ moleculetype ]
; Name nrexcl
CNT 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 opls_145 1 CNT C 1 0 12.011 ; qtot 0
2 opls_145 1 CNT C 2 0 12.011 ; qtot 0
3 opls_145 1 CNT C 3 0 12.011 ; qtot 0
4 opls_145 1 CNT C 4 0 12.011 ; qtot 0
5 opls_145 1 CNT C 5 0 12.011 ; qtot 0
6 opls_145 1 CNT C 6 0 12.011 ; qtot 0
7 opls_145 1 CNT C 7 0 12.011 ; qtot 0
8 opls_145 1 CNT C 8 0 12.011 ; qtot 0
9 opls_145 1 CNT C 9 0 12.011 ; qtot 0
问题5：下面是md模拟的mdp文件，烦请各位老师帮我检查下是否适用于这个体系是否需要更正？
; VARIOUS PREPROCESSING OPTIONS
define =
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0
dt = 0.001
nsteps = 100000000
init_step = 0
comm_mode = Linear
nstcomm = 100
comm-grps = system
; OUTPUT CONTROL OPTIONS
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 2000
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 2020-6-24 23:45:02
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