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zyj8119

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专业: 理论和计算化学

[求助] gromacs做全原子模拟时候，突然到MD这一步出错

MD的控制文件是这样的：
title                   = MD simulation
;Preprocessor
cpp    = /lib/cpp
;Directories to include in the topology format
include    = -I../top
;Run control: A leap-frog algorithm for integrating Newton's equations.
integrator    = md
;Total simulation time: 1000 ps
:time step in femtoseconds
dt    = 0.002
;number of steps
nsteps       = 10000000
;frequency to write coordinates to output trajectory file
nstxout    = 5000
;frequency to write velocities to output trajectory file
nstvout    = 5000
;frequency to write energies to log file
nstlog       = 1000
;frequency to write energies to energy file
nstenergy    = 1000
;frequency to write coordinates to xtc trajectory
nstxtcout    = 1000
;group(s) to write to xtc trajectory
xtc_grps    = OCT
;group(s) to write to energy file
energygrps    = OCT
;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist    = 5
;Make a grid in the box and only check atoms in neighboring grid cells
;when constructing a new neighbor list every nstlist steps.
ns_type    = grid
;cut-off distance for the short-range neighbor list
rlist    = 1.0
;treatment of electrostatic interactions
coulombtype    = PME
rcoulomb    = 1.0
fourierspacing    =0.12
pme_order          =4
ewald_rtol          =1e-5
optimize_fft       =yes
;treatment of van der waals interactions
rvdw    = 1.4
; Periodic boudary conditions in all the directions
pbc                   = xyz
;Temperature coupling
tcoupl       = berendsen
tc-grps    = OCT
tau_t    = 0.1
ref_t    = 290
;Pressure coupling
;Pcoupl       = berendsen
;Pcoupltype             = isotropic
;tau_p    = 1.0
;compressibility    = 4.5e-5
;ref_p    = 1.0
;Velocity generation
gen_vel    = yes
gen_temp    = 290
gen_seed    = 173529
; Type of constraint algorithm
constraint-algorithm    = Lincs
lincs-iter             = 4
;Constrain bonds
constraints    = none

出现的错误是：
creating statusfile for 1 node...
' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
' for variable pbc, using 'xyz'
Next time use one of: 'xyz' 'no' 'full'
' for variable coulombtype, using 'Cut-off'
Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized-Born' 'Reaction-Field-nec' 'Encad-shift' 'PME-User'
' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'
' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen' 'Andersen-interval'
' for variable gen-vel, using 'no'
Next time use one of: 'no' 'yes'
' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
' for variable constraint-algorithm, using 'Lincs'
Next time use one of: 'Lincs' 'Shake'

Fatal error:
number of coordinates in coordinate file (box.pdb, 3900)
         does not match topology (octanebox.top, 0)
top文件在能量最小化的那一步没有任何问题，但是在MD这一步就不行了。

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