[gmx-users] grompp error(Segmentation fault)

[Justin A. Lemkul]

I suppose the next set of questions to ask would be:

1. How was Gromacs compiled?  What options were specified?
2. Does every instance of grompp fail?  Do other inputs work?  What does "grompp 
-h" do?
3. Does grompp seg fault with totally different systems (different force fields)?

-Justin

Arik Cohen wrote:
> 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(2.6.32.11-99.fc12.i686, 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
>                                    tpa
>   -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
>                             sites
> -maxwarn     int    0       Number of allowed warnings during input 
> processing
> -[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
> 
> 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 
> /usr/local/gromacs/share/gromacs/top//ffamber99sbbon.itp
> Segmentation fault (core dumped)
> 
> 
> Thanks a lot in advance for all your help
> 
> Arik
> 
> 
> 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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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