[gmx-users] Segmentation fault with g_order

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 13 13:00:57 CEST 2010

Javier Cerezo wrote:
> Hello
> I tried to run g_order on a cluster with Core 2 Quad Q6600 processor 
> where the Gromacs Suite 4.0.1 has been compiled in single precision. The 
> program stops with a message from the compiler (i.e. in Spanish): 
> "Violación de segmento" (=Segmentation fault, I guess) and I couldn't 
> find an answer neither in the manual nor in the web. The program is run 
> with default parameters on a simulation of a membrane (the index.ndx 
> contains the membrane and the waters). Below, you can find the output. 
> Could someone give a clue about the problem and what to do?

Your index file is wrong.  See here:



> Thanks a lot for your help.
> ---------------------------------------------------------------------------------------------------------------------------------- 
> ---------------------------------------------------------------------------------------------------------------------------------- 
>                               :-)  g_order  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>  -f       traj.xtc  Input        Trajectory: xtc trr trj gro g96 pdb cpt
>  -n      index.ndx  Input        Index file                            
>  -s      topol.tpr  Input        Run input file: tpr tpb tpa           
>  -o      order.xvg  Output       xvgr/xmgr file                        
> -od     deuter.xvg  Output       xvgr/xmgr file                        
> -os     sliced.xvg  Output       xvgr/xmgr file                        
> -Sg     sg-ang.xvg  Output, Opt. xvgr/xmgr file                        
> -Sk    sk-dist.xvg  Output, Opt. xvgr/xmgr file                       
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit -nice        int    
> 19      Set the nicelevel        -b           time   0       First frame 
> (ps) to read from trajectory
> -e           time   0       Last frame (ps) to read from trajectory
> -dt          time   0       Only use frame when t MOD dt = first time (ps)
> -[no]w       bool   no      View output xvg, xpm, eps and pdb files      
> -[no]xvgr    bool   yes     Add specific codes (legends etc.) in the output
>                            xvg files for the xmgrace program             
> -d           enum   z       Direction of the normal on the membrane: z, 
> x or y
> -sl          int    1       Calculate order parameter as function 
> of                                    boxlength, dividing the box in #nr 
> slices.       -[no]szonly  bool   no      Only give Sz element of order 
> tensor. (axis can                             be specified with 
> -d)                            -[no]unsat   bool   no      Calculate 
> order parameters for unsaturated                                  
> carbons. Note that this cannot be mixed with     
>                            normal order parameters.                        
> Taking z axis as normal to the membrane
> Reading file topol.tpr, VERSION 4.0.7 (single precision)
> Using following groups:                                Groupname: DMPC 
> First atomname: C33 First atomnr 0     Groupname: SOL First atomname: OW 
> First atomnr 5888   
> Reading frame       0 time    0.000   Number of elements in first group: 
> 5888
> Reading frame       1 time    0.500   Violación de segmento
> ----------------------------------------------------------------------------------------------------------------------------------------------------------- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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