[gmx-users] grompp error(Segmentation fault)
Justin A. Lemkul
jalemkul at vt.edu
Mon Apr 26 00:21:37 CEST 2010
Arik Cohen wrote:
> 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.
>
You get the seg fault right after ffamber99sbbon.itp is opened. Are there bad
lines in it? In the latest ffamber ports (for version 4.0), there are two files
- "ffamber99sbbon.itp" and "ffamber99sbbon.itp.bad." Perhaps there has been
some pertinent change since you've obtained the ffamber ports. Do other AMBER
force fields work for your system of interest, like ffamber99 or ffamber03? If
so, it would suggest that the integrity of one or more ffamber99sb* files has
been somehow compromised.
-Justin
> 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
>>>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list