[gmx-users] grompp error(Segmentation fault)

Arik Cohen acohen at biochem.duke.edu
Sat Apr 24 22:28:13 CEST 2010

Thank a lot for your very fast response !. Here are the requested details:

1. Version 4.07 is being used.

2. Upgrading from version 4.04 to 4.07 doesn't help.

3. The grompp command given is:

     grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top 
-o 1bgq_Complex_b4ion..tpr

4. em.mdp:

integrator          =  l-bfgs
nsteps              =  50000
nstlist             =  1
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
vdw-type            =  cut-off
rvdw                =  1.0
nstenergy           =  10
emtol            =  5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
define              =  -DFLEXIBLE ; using flexible water model

5. The grompp command is issued in this case, before genion. However, 
even when running it alone the same problem arises.

6. The program is being run on Fedora 12 inside 
VMware(, 32-bit).

7. Running the same command on another OS and type of 
machine(fc10.x86_64) does not solve the problem

7. The output:

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

                      Gnomes, ROck Monsters And Chili Sauce

                             :-)  VERSION 4.0.7  (-:

       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
              Copyright (c) 2001-2008, 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.

                      :-)  grompp_d (double precision)  (-:

Option     Filename  Type         Description
   -f     MDP/em.mdp  Input, Opt!  grompp input file with MD parameters
  -po      mdout.mdp  Output       grompp input file with MD parameters
   -c 1bgq_Complex_b4ion.pdb  Input        Structure file: gro g96 pdb 
tpr tpb
   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
   -n      index.ndx  Input, Opt.  Index file
   -p 1bgq_Complex.top  Input        Topology file
  -pp  processed.top  Output, Opt. Topology file
   -o 1bgq_Complex_b4ion..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: edr ene

Option       Type   Value   Description
-[no]h       bool   no      Print help info and quit
-nice        int    0       Set the nicelevel
-[no]v       bool   yes     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
-maxwarn     int    0       Number of allowed warnings during input 
-[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

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...

WARNING 1 [file MDP/em.mdp, line unknown]:
   For efficient BFGS minimization, use switch/shift/pme instead of cut-off.

processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top//ffamber99sb.itp
Opening library file /usr/local/gromacs/share/gromacs/top//ffamber99sbnb.itp
Opening library file 
Segmentation fault (core dumped)

Thanks a lot in advance for all your help


On 4/23/2010 4:45 PM, Mark Abraham wrote:
> On 24/04/2010 7:28 AM, Arik Cohen wrote:
>> I'll be most thankful if any one would be able to help me with the
>> following problem.
> Giving more complete information will give you a much better chance. 
> It's not our job to be the family doctor and ask questions :-)
> What GROMACS version is it? Does upgrading to 4.0.7 help?
>> While running the grompp (in both single and double precision) command I
>> get a Segmentation fault (core dumped) error.
> When? What was the output to date?
>> The error persist even
>> after recompiling the GROMACS with gcc-4.4.3(previously I was running
>> 4.04 compiled with the buggy gcc-4.1 compiler).
> Does it happen on another machine?
>> The command I'm using is:
>> grompp_d -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top -o
>> 1bgq.tpr
> What's in the .mdp file?
> Mark

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