[gmx-users] Re:Crash error

[Justin A. Lemkul]

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

-- 
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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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