[gmx-users] Segmentation fault with g_order

Javier Cerezo jcb1 at um.es
Tue Apr 13 11:43:55 CEST 2010


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?

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 
                            boxlength, dividing the box in #nr 
-[no]szonly  bool   no      Only give Sz element of order tensor. (axis 
                            be specified with 
-[no]unsat   bool   no      Calculate order parameters for 
                            carbons. Note that this cannot be mixed 
                            normal order 

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: 
Reading frame       1 time    0.500   Violación de segmento

Dpto. Química-Física
Universidad de Murcia
30100 Murcia (SPAIN)

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