标题: 求助：使用gromacs进行蛋白质分子动力学模拟到160ns时系统崩溃 [打印本页] 作者Author: wwl 时间: 2021-6-7 17:28 标题: 求助：使用gromacs进行蛋白质分子动力学模拟到160ns时系统崩溃 各位老师们好，我在网站上下载的蛋白质pdb文件，删除掉结晶水以后，使用gromacs命令构建的蛋白质盒子，并使用命令添加了10033个水分子，和8个氯离子平衡电荷，模拟进行了160ns的时候，系统突然崩溃，out文件中出现如下的报错：36 particles communicated to PME rank 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.
我的md.mdp文件如下所示：
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 2500000 ; 2 * 500000 = 1000 ps (1 ns)
dt = 0.001 ; 2 fs
comm-grps = Protein
comm-mode = angular
; Output control
nstxout = 5000 ; save coordinates every 10.0 ps
nstvout = 5000 ; save velocities every 10.0 ps
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
; nstxout-compressed replaces nstxtcout
compressed-x-grps = System ; replaces xtc-grps
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-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 = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; 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 on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.2 0.2 ; time constant, in ps
ref_t = 358 358 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in 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 ; Velocity generation is off