[gmx-users] linux crash
Thil Batuwangala
thil at strubi.ox.ac.uk
Wed Apr 2 18:08:01 CEST 2003
well, I am basically following the Jonhn Kerrigan tutorial word for word
... all programs run fine so I am not suspecting any of the input files.
my mdout.mdp looks like this:
************************************************
;
; File 'mdout.mdp' was generated
; By user: thil (1027)
; On host: spritzer
; At date: Wed Apr 2 12:45:01 2003
;
; VARIOUS PREPROCESSING OPTIONS =
title = Yo
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0
dt = 0.002
nsteps = 10000
; 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 =
; 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
; Step size (1/ps^2) for minimization of flexible constraints =
fcstep = 0
; 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 = 0
nstfout = 0
; 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 or no =
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
; 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 = 0.9
; 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-5
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
Tcoupl = berendsen
; Groups to couple separately =
tc-grps = protein drg sol
; Time constant (ps) and reference temperature (K) =
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Pressure coupling =
Pcoupl = no
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 = yes
gen_temp = 300.0
gen_seed = 173529
; OPTIONS FOR BONDS =
constraints = hbonds
; 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 = 1e-04
; 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: 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) to energy file =
nstorireout = 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
*****************************************************************
do you need more details about the linux box I am using ?
thanks
t.
Christoph Freudenberger wrote:
> Thil Batuwangala wrote:
>
>> I am following Jonhn Kerrigan's tutorial (from the PRODRG site) for
>> protein-ligand model. every thing runs fine, except that MDRUN
>> crashes half way through. I am running GROMACS on a linux machine. I
>> just get a "segmentation fault (core dumped)" message ..... which
>> does not tell you much about what is crashing.
>>
>> anyone else had this problem ?
>>
> sure... can have a number of reasons.
>
> Please give more details.
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