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吉米爱多

铁杆木虫 (著名写手)

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注册: 2013-03-04
专业: 能源化工

[交流] 采用semiisotropic压力耦合，xy方向压力不可控

我的体系是图1，npt阶段的mdp参数设置如下：
define = -DFLEXIBLE -DPOSRES ; position restrain
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 10000000 ; 10 ns
dt = 0.001 ; 1 fs
; Output control
nstxout = 5000
nstvout = 5000
nstenergy = 5000
nstlog = 5000
; Bond parameters
continuation = yes
constraint_algorithm  = lincs ; holonomic constraints
constraints = h-bonds
lincs_iter    = 1       ; accuracy of LINCS
lincs_order    = 4       ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
rlist          = 1
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 10 fs, largely irrelevant with Verlet
rcoulomb = 1 ; short-range electrostatic cutoff (in nm)
rvdw = 1 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME          ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = v-rescale ; modified Berendsen thermostat
tc-grps = mmt notmmt ; two coupling groups - more accurate
tau_t = 2.0 2.0       ; time constant, in ps
ref_t = 250 250          ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = berendsen       ; Pressure coupling on in NPT
pcoupltype = semiisotropic
tau_p = 4.0 4.0             ; time constant, in ps
ref_p = 500.0 500.0             ; reference pressure, in bar
compressibility = 0 4.5e-5             ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off

10ns的npt结束后压力是图2。可见z方向的压力控制得比较好，在500bar附近波动。但是xy方向的压力非常大，完全控制不了。
我试过将xy方向的耦合压力改成0，结果也还是有很大的压力。
请问大家，采用semiisotropic压力耦合时，需要考虑xy方向的压力吗，还是只考虑z方向压力就可以了呢？

蒙脱石孔隙水.jpg