我做粗粒化的过程中，用NVT系综就可以通过，但是一用NPT就会出现好多问题，有时说CUT-OFF值大于盒子一半，我调了之后就会出现体系崩溃，要不就是盒子漂移了，等等，想问大家遇到过这种情况？都怎么解决的 ，需要调节哪些参数吗？是多链体系，盒子大小为4.2*4.2*4.2.下面是我的mdp文件
; RUN CONTROL PARAMETERS
integrator= md
; Start time and timestep in ps
tinit= 0
dt= 0.001
nsteps= 1000000
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= linear
; number of steps for center of mass motion removal
nstcomm= 1
; group(s) for center of mass motion removal
comm-grps= system
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric= 0
ld-seed= 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 10
emstep= 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (ps^2) for minimization of flexible constraints
fcstep= 0
; Frequency of steepest descents steps when doing CG
nstcgsteep= 1000
nbfgscorr= 10
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist= 1.0
; ns algorithm (simple or grid)
ns_type= grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc= xyz
; nblist cut-off
rlist= 1
domain-decomposition= no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype= cut-off
rcoulomb-switch= 0
rcoulomb= 1
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf= 1
; Method for doing Van der Waals
vdw-type= cut-off
; cut-off lengths
rvdw-switch= 0
rvdw= 1
; Apply long range dispersion corrections for Energy and Pressure
DispCorr= No
; Extension of the potential lookup tables beyond the cut-off
table-extension= 10
; Seperate tables between energy group pairs
energygrp_table=
; Spacing for the PME/PPPM FFT grid
fourierspacing= 0.12
; 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-5
ewald_geometry= 3d
epsilon_surface= 0
optimize_fft= yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl= nose-hoover
; Groups to couple separately
tc_grps= system
; Time constant (ps) and reference temperature (K)
tau_t= 0.3
ref_t= 300
; Pressure coupling
Pcoupl= no
arrinello-Rahman
pcoupltype= isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 0.5
compressibility= 6.5e-5
ref_p= 1.0
; Random seed for Andersen thermostat
andersen_seed= 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel= yes
gen_temp= 300
gen-seed= 173529

1.你的盒子里面是不是满的。
2.可以做一个大一点的。你的粗粒化嘛，做到8nm没有问题，这样就不会迅速减小到3一下。
3.你的 问题可能是压缩导致xy方向的盒子尺度减小。从正方体转变为长方体，你可以改下压缩条件什么的。看看你的结果动画，是不是发生尺度变化。

谢谢楼上，我看看动画

你好，我现在也在学习粗粒化模拟，能加我QQ么？QQ：768511461

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