[gmx-users] Segmentation error (core dump)

Shichen wang longmissw at email.jlu.edu.cn
Sun Jan 14 07:56:48 CET 2007

Dear gmx-users,

I installed the gromacs-3.3.1 on Cygwin and no problems occured, but when I execute the commands such as g_angle,pdb2gmx, all commands gave the message: Segmentation fault (core dumped) at the end. Anybody have met this problem ever? How to resolve it?
Thanks for any advises.

$ g_angle
                         :-)  G  R  O  M  A  C  S  (-:

             Gallium Rubidium Oxygen Manganese Argon Carbon Silicon

                            :-)  VERSION 3.3.1  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2006, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                               :-)  g_angle  (-:

Option     Filename  Type         Description
  -f       traj.xtc  Input        Generic trajectory: xtc trr trj gro g96 pdb
  -s      topol.tpr  Input        Generic run input: tpr tpb tpa xml
  -n      angle.ndx  Input        Index file
 -od    angdist.xvg  Output       xvgr/xmgr file
 -ov    angaver.xvg  Output, Opt. xvgr/xmgr file
 -of    dihfrac.xvg  Output, Opt. xvgr/xmgr file
 -ot   dihtrans.xvg  Output, Opt. xvgr/xmgr file
 -oh    trhisto.xvg  Output, Opt. xvgr/xmgr file
 -oc    dihcorr.xvg  Output, Opt. xvgr/xmgr file
 -or       traj.trr  Output, Opt. Trajectory in portable xdr format

      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
-[no]periodic  bool    yes  Print dihedral angles modulo 360 degrees
-[no]chandler  bool     no  Use Chandler correlation function (N[trans] = 1,
                            N[gauche] = 0) rather than cosine correlation
                            function. Trans is defined as phi < -60 || phi >
-[no]avercorr  bool     no  Average the correlation functions for the
                            individual angles/dihedrals
     -acflen    int     -1  Length of the ACF, default is half the number of
-[no]normalize bool    yes  Normalize ACF
          -P   enum      0  Order of Legendre polynomial for ACF (0 indicates
                            none): 0, 1, 2 or 3
      -fitfn   enum   none  Fit function: none, exp, aexp, exp_exp, vac,
                            exp5, exp7 or exp9
     -ncskip    int      0  Skip N points in the output file of correlation
   -beginfit   real      0  Time where to begin the exponential fit of the
                            correlation function
     -endfit   real     -1  Time where to end the exponential fit of the
                            correlation function, -1 is till the end

Segmentation fault (core dumped)


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