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吉米爱多铁杆木虫 (著名写手)
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采用semiisotropic压力耦合，xy方向压力不可控
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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  压力.png |
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2楼2019-04-25 16:33:24
吉米爱多
铁杆木虫 (著名写手)
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