[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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