[gmx-users] Arithmetic Exception (core dumped)
Lianqing Zheng
lzheng at me.rochester.edu
Wed May 8 23:06:49 CEST 2002
My fs.mdp file is attached. Thanks.
Lianqing
On Wed, 8 May 2002, David van der Spoel wrote:
>On Wed, 8 May 2002, Lianqing Zheng wrote:
>
>>Dear all:
>>
>>I got an error of "Arithmetic Exception" when running mdrun. I tried to
>>use gdb to find where the program broke, and it says:
>>(gdb) where
>>#0 0x6f1ac in make_tables ()
>>#1 0x4a9f4 in init_forcerec ()
>>#2 0x324e0 in mdrunner ()
>>#3 0x22e88 in main ()
>>
>>But I couldn't get which line it is. What do you think of this?
>depends on your input. Send us your mdp file. Or do you try to read a user
>table?
>
>>
>
>Groeten, David.
>________________________________________________________________________
>Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
>Husargatan 3, Box 576, 75123 Uppsala, Sweden
>phone: 46 18 471 4205 fax: 46 18 511 755
>spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
-------------- next part --------------
;
; File 'fs.mdp' was generated
; By user: zheng (1223)
; On host: ironwood
; At date: Mon Apr 22 15:20:47 2002
;
; VARIOUS PREPROCESSING OPTIONS =
title = Yo
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0
dt = 0.001
nsteps = 10000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps =
; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
bd-temp = 300
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol = 100
emstep = 0.01
; Max number of iterations in relax_shells =
niter = 20
; Frequency of steepest descents steps when doing CG =
nstcgsteep = 1000
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 500
nstvout = 10000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 50
nstenergy = 50
; 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 = simple
; Periodic boundary conditions: xyz or no =
pbc = xyz
; nblist cut-off =
rlist = 0.7
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 0.7
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r = 1
; Method for doing Van der Waals =
vdw-type = Cut-off
; cut-off lengths =
rvdw-switch = 0
rvdw = 0.7
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; 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-05
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
Tcoupl = berendsen
; Groups to couple separately =
tc-grps = System
; Time constant (ps) and reference temperature (K) =
tau_t = 0.1
ref_t = 7000
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; SIMULATED ANNEALING CONTROL =
annealing = no
; Time at which temperature should be zero (ps) =
zero-temp_time = 0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 7000
gen_seed = 1993
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start = no
; Relative tolerance of shake =
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order = 4
; 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: Equal or Conservative =
disre-weighting = Equal
; 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
; Free energy control stuff =
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff =
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
; 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
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