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zhlrui

银虫 (小有名气)

应助: 0 (幼儿园)
金币: 523.4
散金: 10
红花: 1
帖子: 146
在线: 23.5小时
虫号: 452350
注册: 2007-11-05
性别: MM
专业: 生物化学

[交流] [交流讨论]关于膜蛋白能量最小化的问题

[交流讨论]关于膜蛋白能量最小化的问题

请大家帮忙，非常感谢！
我的体系是由四部分的离子通道膜蛋白加DOPC双层膜组成，选择gromacs力场，进行能量最小化，也就是第一个mdrun时，有以下出错信息：
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 24389 ]
Please report this to the mailing list (gmx-users@gromacs.org)

怎么回事啊？
[search]膜蛋白 DOPC膜 gromacs[/search]

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为了理想而奋斗

1楼 2008-09-17 19:26:46

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zhlrui

银虫 (小有名气)

应助: 0 (幼儿园)
金币: 523.4
散金: 10
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在线: 23.5小时
虫号: 452350
注册: 2007-11-05
性别: MM
专业: 生物化学

有高手说应该是参数设置问题，下面是我的mdout.mdp
title                   = comp_dop_water
; Preprocessor - specify a full path if necessary.
cpp                   = /lib/cpp
include                =
define                = -DFLEX_SPC

; RUN CONTROL PARAMETERS
integrator             = steep
; Start time and timestep in ps
tinit                   = 0
dt                      = 0.002
nsteps                = 3000
; 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             =

; 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                   = 1000.0
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

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                = 100
nstvout                = 100
nstfout                = 0
; Checkpointing helps you continue after crashes
nstcheckpoint          = 1000
; Output frequency for energies to log file and energy file
nstlog                = 100
nstenergy             = 100
; Output frequency and precision for xtc file
nstxtcout             = 0
xtc-precision          = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps                =
; Selection of energy groups
energygrps             =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                = 10
; 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                   = 0.9
domain-decomposition    = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype             = PME
rcoulomb-switch       = 0
rcoulomb                = 0.9
; 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                   = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                = No
; Extension of the potential lookup tables beyond the cut-off
table-extension       = 1
; 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

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm          = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii             = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                = 2
; Salt concentration in M for Generalized Born models
gb_saltconc             = 0

; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
implicit_solvent       = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl                = No
; Groups to couple separately
tc-grps                =
; Time constant (ps) and reference temperature (K)
tau-t                   =
ref-t                   =
; Pressure coupling
Pcoupl                = No
Pcoupltype             = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p                   = 1
compressibility       =
ref-p                   =
; Random seed for Andersen thermostat
andersen_seed          = 815131

; OPTIONS FOR QMMM calculations
QMMM                   = no
; Groups treated Quantum Mechanically
QMMM-grps             =
; QM method
QMmethod                =
; QMMM scheme
QMMMscheme             = normal
; QM basisset
QMbasis                =
; QM charge
QMcharge                =
; QM multiplicity
QMmult                =
; Surface Hopping
SH                      =
; CAS space options
CASorbitals             =
CASelectrons          =
SAon                   =
SAoff                   =
SAsteps                =
; Scale factor for MM charges
MMChargeScaleFactor    = 1
; Optimization of QM subsystem
bOPT                   =
bTS                   =

; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing             =
; Number of time points to use for specifying annealing in each group
annealing_npoints       =
; List of times at the annealing points for each group
annealing_time          =
; Temp. at each annealing point, for each group.
annealing_temp          =

; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel                = no
gen-temp                = 300
gen-seed                = 173529

; OPTIONS FOR BONDS
constraints             = none
; Type of constraint algorithm
constraint-algorithm    = Lincs
; Do not constrain the start configuration
unconstrained-start    = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR             = no
; Relative tolerance of shake
shake-tol             = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs-order             = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter             = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle       = 30
; Convert harmonic bonds to morse potentials
morse                   = no

; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl          =

; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre                   = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting       = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed             = no
disre-fc                = 1000
disre-tau             = 0
; Output frequency for pair distances to energy file
nstdisreout             = 100
; Orientation restraints: No or Yes
orire                   = no
; Orientation restraints force constant and tau for time averaging
orire-fc                = 0
orire-tau             = 0
orire-fitgrp          =
; Output frequency for trace(SD) and S to energy file
nstorireout             = 100
; Dihedral angle restraints: No, Simple or Ensemble
dihre                   = No
dihre-fc                = 1000
dihre-tau             = 0
; Output frequency for dihedral values to energy file
nstdihreout             = 100

; Free energy control stuff
free-energy             = no
init-lambda             = 0
delta-lambda          = 0
sc-alpha                = 0
sc-power                = 0
sc-sigma                = 0.3

; Non-equilibrium MD stuff
acc-grps                =
accelerate             =
freezegrps             = protein
freezedim             = y y y
cos-acceleration       = 0
deform                =

; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x                   =
E-xt                   =
E-y                   =
E-yt                   =
E-z                   =
E-zt                   =

; User defined thingies
user1-grps             =
user2-grps             =
userint1                = 0
userint2                = 0
userint3                = 0
userint4                = 0
userreal1             = 0
userreal2             = 0
userreal3             = 0
userreal4             = 0

[ Last edited by zhlrui on 2008-9-20 at 09:33 ]