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

[Justin A. Lemkul]

deisy yurley rodriguez sarmiento wrote:
> 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.
> 

Well, a seg fault could be due to a large number of factors, although the .mdp 
file is helpful.  Generic information can be found here:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

If you can provide more detail on what your system is, how you built it, what 
Gromacs version you're using, and the success of energy minimization and 
equilibration, that will help.  Other comments are embedded within the .mdp file 
itself.

> title                    =
> cpp                      = /usr/bin/cpp
> include                  =
> define                   = -DFLEXIBLE

Never use flexible water when running MD.  It is only useful during energy 
minimization, and doesn't make sense in the context of MD since all the default 
water models are rigid.  For instance:

http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html

Maybe Gromacs should generate a warning about the combination of the md 
integrator and the DFLEXIBLE parameter.

> 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

You've got a combination of distance restraints, dihedral restraints, and free 
energy calculations turned on.  Is your system stable in the absence of all of 
these factors?

-Justin

> 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
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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