[gmx-users] Segmentation fault (core dumped) version 4.6.*

Justin Lemkul jalemkul at vt.edu
Thu May 21 19:50:37 CEST 2015

On 5/21/15 11:55 AM, Carlos Navarro Retamal wrote:
> Dear gmx users,
> In order to run my simulations, i usually used the 5.0.* version of gromacs without problems, but since i want to performed umbrella sampling simulations (and since the option pull_geometry=position is not available for the latest versions)
> For that,  i installed the 4.6.7 version of gromacs.
> The installation went without issue, but every time i used a command from gromacs i got the Segmentation fault (core dumped) error:
> Like for example, by using this command line:
> grompp -f npt_production.mdp -c npt_equilibration.gro -p topol.top -o npt_production.tpr
> i got this:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>    -f npt_production.mdp  Input        grompp input file with MD parameters
>   -po      mdout.mdp  Output       grompp input file with MD parameters
>    -c npt_equilibration.gro  Input        Structure file: gro g96 pdb tpr etc.
>    -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>   -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
>    -n      index.ndx  Input, Opt.  Index file
>    -p      topol.top  Input        Topology file
>   -pp  processed.top  Output, Opt. Topology file
>    -o npt_production.tpr  Output       Run input file: tpr tpb tpa
>    -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>    -e       ener.edr  Input, Opt.  Energy file
> -ref     rotref.trr  In/Out, Opt. Full precision trajectory: trr trj cpt
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    0       Set the nicelevel
> -[no]v       bool   no      Be loud and noisy
> -time        real   -1      Take frame at or first after this time.
> -[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
>                              sites
> -maxwarn     int    0       Number of allowed warnings during input
>                              processing. Not for normal use and may generate
>                              unstable systems
> -[no]zero    bool   no      Set parameters for bonded interactions without
>                              defaults to zero instead of generating an error
> -[no]renum   bool   yes     Renumber atomtypes and minimize number of
>                              atomtypes
> Segmentation fault (core dumped)
> That is not telling me anything useful :/
> I tried also installing the 4.6.3, but sadly i have the same problems with this version.

A seg fault from every tool suggests something fundamentally wrong with your 
GROMACS installation.  Without telling us exactly how you installed it 
(installation commands, compilers, etc.) there's little to suggest.  A gdb 
backtrace could be useful, but again if it's coming from everything there is 
just something totally wrong and not program-specific to debug.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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