[gmx-users] Help with Segmentation fault!!!

[deisy yurley rodriguez sarmiento]

Hi everyone,

I need help because when i run in gromacs, in a few seconds, appears
"segmentation fault" i think that posibly is die to .mdp file. So
is  copied below. thanks in advance.



title                    =

cpp                     
= /usr/bin/cpp

include                  =

define                   = -DFLEXIBLE

integrator               = md

init                     = 0

dt                      
= 0.001

nsteps                   = 500000

init_step                = 0

comm-mode                = Linear

nstcomm                  = 1

comm-grps                =

bd-fric                  = 0

ld-seed                  = 1993

emtol                    = 10

emstep                   = 0.01

niter                    = 20

fcstep                   = 0

nstcgsteep               = 1000

nbfgscorr                = 10

nstxout                  = 100

nstvout                  = 100

nstfout                  = 0

nstcheckpoint            = 1000

nstlog                   = 100

nstenergy                = 100

nstxtcout                = 0

xtc-precision            = 1000

xtc-grps                 =

energygrps               =

nstlist                  = 10

ns_type                  = simple

pbc                     
= xyz

rlist                    = 1

domain-decomposition     = no

coulombtype              = shift

rcoulomb-switch          = 0.9

rcoulomb                 = 1.0

epsilon_r                = 1

epsilon_rf               = 1

vdw-type                 = Cut-off

rvdw-switch              = 0

rvdw                    
= 1.0

DispCorr                 = No

table-extension          = 1

energygrp_table          =

fourierspacing           = 0.12

fourier_nx               = 0

fourier_ny               = 0

fourier_nz               = 0

pme_order                = 4

ewald_rtol               = 1e-05

ewald_geometry           = 3d

epsilon_surface          = 0

optimize_fft             = no

gb_algorithm             = Still

nstgbradii               = 1

rgbradii                 = 2

gb_saltconc              = 0

implicit_solvent         = No

Tcoupl                   = no

tc-grps                  =

tau-t                    =

ref-t                    =

Pcoupl                   = no

Pcoupltype               = Isotropic

tau-p                    = 1

compressibility          =

ref-p                    =

andersen_seed            = 815131

QMMM                    
= no

QMMM-grps                =

QMmethod                 =

QMMMscheme               = normal

QMbasis                  =

QMcharge                 =

QMmult                   =

SH                      
=

tions                    =

CASorbitals              =

CASelectrons             =

SAon                     =

SAoff                    =

SAsteps                  =

MMChargeScaleFactor      = 1

bOPT                     =

bTS                     
=

annealing                =

annealing_npoints        =

annealing_time           =

annealing_temp           =

gen_vel                  = no

gen-temp                 = 300

gen-seed                 = 173529

constraints              = none

constraint-algorithm     = Lincs

unconstrained-start      = no

Shake-SOR                = no

shake-tol                = 0.0001

lincs-order              = 4

lincs-iter               = 1

lincs-warnangle          = 30

morse                    = no

energygrp_excl           =

disre                    = simple

disre-weighting          = Conservative

disre-mixed              = no

disre_fc                 = 1200

disre-tau                = 0

nstdisreout              = 100

orire                    = no

orire-fc                 = 0

orire-tau                = 0

orire-fitgrp             =

nstorireout              = 100

dihre                    = simple

dihre-fc                 = 100

dihre-tau                = 0.0

nstdihreout              = 50

free-energy              = yes

init-lambda              = 0

delta-lambda             = 0

sc-alpha                 = 0.5

sc-power                 = 1.0

sc-sigma                 = 0.3

acc-grps                 =

accelerate               =

freezegrps               =

freezedim                =

cos-acceleration         = 0

deform                   =

E-x                     
=

E-xt                     =

E-y                     
=

E-yt                     =

E-z                     
=

E-zt                     
=

user1-grps             =

user2-grps             =

userint1                 = 0

userint2                 = 0

userint3                 = 0

userint4                 = 0

userreal1               = 0




Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
Tel. 6344000  ext. 2792
Universidad Industrial de Santander



      
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