[gmx-users] grompp error(Segmentation fault)
Arik Cohen
acohen at biochem.duke.edu
Mon Apr 26 00:07:47 CEST 2010
In continuation with my previous e-mail, I'm sorry to continue bothering
you with this but after reevaluating, it seems that problem might just
be with the amber forcefield after all as I manged to run grompp just
fine and to start the minimization by applying the OPLS forcefield(with
another OPLS compatible protein: bpti).
I'm still interested in running my program with the amber forcefiled as
to be compatible with other calculations being done in the group.
I would be most thankful for any suggestion you might have.
Thanks a lot
Arik
On 4/24/2010 5:23 PM, Arik Cohen wrote:
> Thanks again for the ultrafast response.
>
> 1. The extra '.' is a typo. (I apologize for that). In the command the
> file name appears as 1bgq_Complex_b4ion.tpr
> in addition, Both the single precision and double
> precision(grompp_d) gives this error.
> The compilation was done with gcc-4.4.3 with and without the
> option of --disable-float for the double and single precision
> version respectively.
>
> 2a. This is the first call to grompp
>
> b. The following programs such as pdb2gmx_d, editconf_d and genbox are
> working properly.
>
> c.grompp/_d -h is working , giving a description on the program with
> the different options available.
>
> 3. With regards of running grompp with different forcefield
>
> *Apparently the problem is with the l-bfgs option in the em.mdp file.
> This is due to the fact that when changing the integrator option to
> steep, the program runs fine *
>
> I'm sorry but I just saw this now.
>
> The l-bfgs integrator was chosen since I need to do normal mode analysis
>
> Thanks a lot
>
> Arik
>
>
> On 4/24/2010 2:26 PM, Justin A. Lemkul wrote:
>> 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
>>
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