[gmx-users] Re:RE:Crash error

[lloyd riggs]

Dear Justin,

Thank you, that's the first help I have had.  In any case, I will look at the .mdp file , as I was using a test structure I already ran through an MD.  I had gone from 4.0.7 to 4.5.1 to 4.5.3, the first two ran MD's.  Now I am rolling back too 4.0.7, but have not recieved complaints from the software in preperation other then rlistlong not found, etc...and the posted errors


> Message: 6
> Date: Tue, 21 Dec 2010 15:25:06 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re:Crash error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D110D22.5040803 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> 
> 
> lloyd riggs wrote:
> > Dear All,
> > 
> > I had posted part of the error below.  I still have not the problem
> solved, everything from gromacs runs, including short energy minimizations, but
> if I run an MD I get the log ending;
> > 
> > Started mdrun on node 0 Thu Dec  9 16:56:10 2010
> > 
> >            Step           Time         Lambda
> >               0        0.00000        0.00000
> > 
> > Grid: 10 x 10 x 10 cells
> > Long Range LJ corr.: <C6> 2.3566e-03
> > Long Range LJ corr.: Epot    -59.767, Pres:  -0.198483, Vir:    29.8835
> >    Energies (kJ/mol)
> >         G96Bond       G96Angle    Proper Dih.  Improper Dih.         
> LJ-14
> >     1.19873e+04    5.04804e+03    5.15110e+03    1.67253e+03   
> 1.49605e+00
> >      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)       RF
> excl.
> >     1.15200e+05    2.87676e+09   -5.97670e+01   -1.24355e+05  
> -7.20279e+04
> >       Potential    Kinetic En.   Total Energy    Temperature Pressure
> (bar)
> >     2.87670e+09    4.35260e+17    4.35260e+17    4.13944e+15   
> 9.63648e+14
> > 
> > ________________________
> > 
> > and the error log;
> > 
> > 
> > Reading file
> /home/ubelix/l_insel_ria/l_watkins/gormacswork/Test4gromacs/md1.tpr, VERSION 4.0.7 (double precision)
> > starting mdrun 'Protein'
> > 100000 steps,    200.0 ps.
> > [cnode33:13647] *** Process received signal ***
> > [cnode33:13647] Signal: Segmentation fault (11)
> > [cnode33:13647] Signal code: Address not mapped (1)
> > [cnode33:13647] Failing at address: 0x237fa90
> > [cnode33:13647] [ 0] /lib/libpthread.so.0(+0xf010) [0x2b6e69c97010]
> > [cnode33:13647] [ 1] /usr/lib/libgmx_mpi_d.so.5(+0x115564)
> [0x2b6e69491564]
> > [cnode33:13647] *** End of error message ***
> > 
> > I am trying still to find out how to fix it, and if it is a problem with
> the two files listed, or they are just the last ones called.
> > 
> 
> Your system is blowing up.  Since it's happening at step 0, it's likely
> due to 
> some physically unreasonable geometry.  Note that temperature, pressure,
> etc are 
> all astronomically high.
> 
> Whatever your previous preparation steps (minimization, equilibration),
> they 
> were likely insufficient.  Otherwise, your .mdp file settings are creating
> the 
> problem.
> 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> 
> -Justin
> 
> > Hollidays
> > 
> > Stephan Watkins
> 
> -- 
> ========================================
> 
> 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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