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xueer小雯

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注册: 2013-03-05
专业: 药物设计与药物信息

[求助] 求助：Gromacs平衡时蛋白跑出盒子了，怎么办？已有2人参与

图片3是进行md之前的蛋白与盒子状态，即npt结束后。
图片2是md 20ns后的状态，蛋白几乎全都出去了，盒子中的是小分子。

md.mdp 如下，请高人帮我看看怎么回事，我之前从来没遇到过这样的问题。。。
title    = Protein-ligand complex NVT equilibration
; Run parameters
integrator  = md       ; leap-frog integrator
nsteps    = 10000000 ; 2 * 10000000 = 20000 ps (20 ns)
dt       = 0.002    ; 2 fs
; Output control
nstxout    = 1000       ; suppress .trr output
nstvout    = 1000       ; suppress .trr output
nstenergy = 1000    ; save energies every 2 ps
nstlog    = 1000    ; update log file every 2 ps
nstxtcout = 1000    ; write .xtc trajectory every 2 ps
energygrps  = Protein NAD
; Bond parameters
continuation = yes          ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints    = all-bonds    ; all bonds (even heavy atom-H bonds) constrained
lincs_iter    = 1          ; accuracy of LINCS
lincs_order    = 4          ; also related to accuracy
; Neighborsearching
ns_type    = grid    ; search neighboring grid cells
nstlist    = 5       ; 10 fs
rlist    = 0.9    ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9    ; short-range electrostatic cutoff (in nm)
rvdw       = 1.4    ; 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
tcoupl    = V-rescale                   ; modified Berendsen thermostat
tc-grps    = Protein_NAD Water_and_ions ; two coupling groups - more accurate
tau_t    = 0.1 0.1                   ; time constant, in ps
ref_t    = 298 298                   ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl    = Parrinello-Rahman          ; pressure coupling is on for NPT
pcoupltype  = isotropic                   ; uniform scaling of box vectors
tau_p    = 2.0                         ; time constant, in ps
ref_p    = 1.0                         ; reference pressure, in bar
compressibility = 4.5e-5                   ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc       = xyz    ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel    = no       ; assign velocities from Maxwell distribution

多谢啊！

2.PNG