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我的体系是真空中一个PS薄膜,之前通过各位指点采用deform设置,在x方向上对盒子进行延长进而减小压强,起到对film拉伸的目的,目前已经得到了我想要的结果,但是我需要对拉伸这个过程中film的力学性能进行表征,比如这一过程中film受到的应力是多少,怎么计算的?各位大佬有无相关的方法或文献?谢谢指点!
附上我的mdp参数以及拉伸前后的gro文件
mdp:
title = OPLS MD simulation
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 25000000 ; 2 * 25000000 = 50000000 fs (50 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 50000 ; save coordinates every 500 ps
nstvout = 50000 ; save velocities
nstenergy = 50000 ; save energies
nstlog = 50000 ; update log file
nstxout-compressed = 50000 ; save compressed coordinates
; nstxout-compressed replaces nstxtcout;
compressed-x-grps = System ; replaces xtc-grps
; Bond parameters
continuation = no ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; h-bonds constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is off
tcoupl = no ; modified Berendsen thermostat
tc-grps = System ; three coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; 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 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, in bar
compressibility = 0 4.5e-5 ; isothermal compressibility of water, bar^-1
deform=0.01 0 0 0 0 0
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
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after.zip
336.05 KB, 下载次数 Times of downloads: 10
gro文件
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before.zip
624.37 KB, 下载次数 Times of downloads: 8
gro文件
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